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MongoDB implementation
javild edited this page Nov 17, 2016
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CellBase creates one MongoDB database per species and assembly. Databases are named as follows:
cellbase_<species>_<assembly>_<cellbase-version>
For example:
cellbase_hsapiens_grch37_v4
cellbase_hvulgare_030312v2_v3
cellbase_lmajor_asm272v2_v3
cellbase_mmusculus_grcm38_v3
...
Please, note that the assembly identifier appears with all letters in lowercase and without hyphens or dots. A number of collections are created within each database, not all of them will be available for all species depending on the available data for each species:
gene
genome_info
genome_sequence
conservation
protein
protein_functional_prediction
protein_protein_interaction
regulatory_region
variation
clinical (only available for Human)
MongoDB is by definition schema-less, although documents stored under the same collection will obviously tend to have the same structure. Indexes design is based on expected most frequent queries.
Please find below collection schemas and examples of documents stored in each collection:
- gene
- genome_info
- genome_sequence
- conservation
- protein
- protein_functional_prediction
- protein_protein_interaction
- regulatory_region
- variation
- clinical
Contains gene core annotation (chromosome, start, end, transcripts, exons, etc.), but also data regarding gene-drug interactions, gene expression, etc.
{
"properties": {
"_chunkIds": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"biotype": {
"type": "string"
},
"chromosome": {
"type": "string"
},
"description": {
"type": "string"
},
"end": {
"type": "integer"
},
"expressionValues": {
"items": [
{
"properties": {
"experimentId": {
"type": "string"
},
"experimentalFactor": {
"type": "string"
},
"expression": {
"type": "string"
},
"factorValue": {
"type": "string"
},
"geneName": {
"type": "string"
},
"pvalue": {
"type": "number"
},
"technologyPlatform": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"id": {
"type": "string"
},
"name": {
"type": "string"
},
"source": {
"type": "string"
},
"start": {
"type": "integer"
},
"status": {
"type": "string"
},
"strand": {
"type": "string"
},
"transcripts": {
"items": [
{
"properties": {
"annotationFlags": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"biotype": {
"type": "string"
},
"cDnaSequence": {
"type": "string"
},
"cdnaCodingEnd": {
"type": "integer"
},
"cdnaCodingStart": {
"type": "integer"
},
"cdsLength": {
"type": "integer"
},
"chromosome": {
"type": "string"
},
"end": {
"type": "integer"
},
"exons": {
"items": [
{
"properties": {
"cdnaCodingEnd": {
"type": "integer"
},
"cdnaCodingStart": {
"type": "integer"
},
"cdsEnd": {
"type": "integer"
},
"cdsStart": {
"type": "integer"
},
"chromosome": {
"type": "string"
},
"end": {
"type": "integer"
},
"exonNumber": {
"type": "integer"
},
"genomicCodingEnd": {
"type": "integer"
},
"genomicCodingStart": {
"type": "integer"
},
"id": {
"type": "string"
},
"phase": {
"type": "integer"
},
"sequence": {
"type": "string"
},
"start": {
"type": "integer"
},
"strand": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"genomicCodingEnd": {
"type": "integer"
},
"genomicCodingStart": {
"type": "integer"
},
"id": {
"type": "string"
},
"name": {
"type": "string"
},
"proteinID": {
"type": "string"
},
"proteinSequence": {
"type": "string"
},
"start": {
"type": "integer"
},
"status": {
"type": "string"
},
"strand": {
"type": "string"
},
"xrefs": {
"items": [
{
"properties": {
"dbDisplayName": {
"type": "string"
},
"dbName": {
"type": "string"
},
"id": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'status': 'KNOWN', 'end': 31381608, 'name': 'SDC3', 'source': 'Ensembl', 'strand': '-', '_chunkIds': ['1_6268_5k', '1_6269_5k', '1_6270_5k', '1_6271_5k', '1_6272_5k', '1_6273_5k', '1_6274_5k', '1_6275_5k', '1_6276_5k'], 'start': 31342314, 'biotype': 'protein_coding', 'expressionValues': [{'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-37', 'factorValue': 'placenta', 'expression': 'DOWN', 'pvalue': 0.0051201354}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-37', 'factorValue': 'lung', 'expression': 'UP', 'pvalue': 0.043737635}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-37', 'factorValue': 'pancreas', 'expression': 'DOWN', 'pvalue': 0.020176584}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-37', 'factorValue': 'pharynx', 'expression': 'DOWN', 'pvalue': 0.046227384}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-37', 'factorValue': 'skin', 'expression': 'UP', 'pvalue': 6.5437167e-10}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-37', 'factorValue': 'uterus', 'expression': 'UP', 'pvalue': 0.0001408416}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-6573', 'factorValue': 'placenta', 'expression': 'DOWN', 'pvalue': 0.018525625}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-6573', 'factorValue': 'decidua', 'expression': 'UP', 'pvalue': 0.001570094}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-17539', 'factorValue': 'skin', 'expression': 'DOWN', 'pvalue': 0.032277983}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'trigeminal ganglion', 'expression': 'UP', 'pvalue': 2.354071e-07}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'thymus', 'expression': 'DOWN', 'pvalue': 0.000259607}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'parietal lobe', 'expression': 'UP', 'pvalue': 8.658513e-06}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'pancreas', 'expression': 'DOWN', 'pvalue': 0.0071172626}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'corpus callosum', 'expression': 'UP', 'pvalue': 2.0975715e-05}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'subthalamic nucleus', 'expression': 'UP', 'pvalue': 7.806487e-09}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'midbrain', 'expression': 'UP', 'pvalue': 8.140746e-05}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'dorsal root ganglion', 'expression': 'UP', 'pvalue': 9.337685e-06}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'pituitary gland', 'expression': 'DOWN', 'pvalue': 0.0077369753}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'testis', 'expression': 'DOWN', 'pvalue': 3.08037e-17}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'spleen', 'expression': 'UP', 'pvalue': 0.00036590616}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'hypothalamus', 'expression': 'UP', 'pvalue': 1.4975546e-15}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'medulla', 'expression': 'UP', 'pvalue': 3.9396928e-13}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'myometrium', 'expression': 'UP', 'pvalue': 8.5559164e-11}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'thalamus', 'expression': 'UP', 'pvalue': 3.9065245e-08}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'skeletal muscle', 'expression': 'DOWN', 'pvalue': 1.6489518e-07}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'cerebral cortex', 'expression': 'UP', 'pvalue': 2.6040384e-06}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'bone marrow', 'expression': 'DOWN', 'pvalue': 1.7366887e-05}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'occipital lobe', 'expression': 'UP', 'pvalue': 7.936557e-05}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'spinal cord', 'expression': 'UP', 'pvalue': 4.0106204e-20}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'jejunum', 'expression': 'DOWN', 'pvalue': 0.014048714}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'hippocampus', 'expression': 'UP', 'pvalue': 1.353011e-06}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'thyroid gland', 'expression': 'DOWN', 'pvalue': 0.020842}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'salivary gland', 'expression': 'DOWN', 'pvalue': 0.007536594}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'amygdala', 'expression': 'UP', 'pvalue': 2.641141e-13}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'ventral tegmental area', 'expression': 'UP', 'pvalue': 4.6068708e-11}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'adrenal gland cortex', 'expression': 'UP', 'pvalue': 6.024702e-10}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'trachea', 'expression': 'DOWN', 'pvalue': 0.008862185}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'vulva', 'expression': 'DOWN', 'pvalue': 1.9562876e-05}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'substantia nigra pars compacta', 'expression': 'UP', 'pvalue': 8.931348e-11}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'tongue', 'expression': 'DOWN', 'pvalue': 0.0012368818}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'skin', 'expression': 'UP', 'pvalue': 0.006813136}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'temporal lobe', 'expression': 'UP', 'pvalue': 2.0233852e-06}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'tonsil', 'expression': 'DOWN', 'pvalue': 7.0418486e-05}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'brain', 'expression': 'UP', 'pvalue': 0.0011998765}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'prostate', 'expression': 'DOWN', 'pvalue': 4.8354277e-06}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'ovary', 'expression': 'DOWN', 'pvalue': 0.010235655}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'kidney', 'expression': 'DOWN', 'pvalue': 0.016107103}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'lymph node', 'expression': 'UP', 'pvalue': 9.117638e-05}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'deltoid muscle', 'expression': 'DOWN', 'pvalue': 2.5611981e-16}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'substantia nigra', 'expression': 'UP', 'pvalue': 1.0689047e-10}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'frontal lobe', 'expression': 'UP', 'pvalue': 3.7341495e-06}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-7307', 'factorValue': 'heart ventricle', 'expression': 'DOWN', 'pvalue': 0.044484634}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-2665', 'factorValue': 'lymph node', 'expression': 'UP', 'pvalue': 0.00018994037}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-2665', 'factorValue': 'tonsil', 'expression': 'DOWN', 'pvalue': 0.00018994037}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'groups_369', 'experimentId': 'E-MTAB-62', 'factorValue': 'epidermis', 'expression': 'DOWN', 'pvalue': 0.041385856}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'groups_369', 'experimentId': 'E-MTAB-62', 'factorValue': 'brain', 'expression': 'UP', 'pvalue': 0.0}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'placenta', 'expression': 'DOWN', 'pvalue': 0.0038298161}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'muscle', 'expression': 'UP', 'pvalue': 3.1947636e-08}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'lung', 'expression': 'DOWN', 'pvalue': 0.012748965}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'groups_96', 'experimentId': 'E-MTAB-62', 'factorValue': 'frontal cortex', 'expression': 'UP', 'pvalue': 2.893806e-29}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'blood_nonblood_meta_groups', 'experimentId': 'E-MTAB-62', 'factorValue': 'blood', 'expression': 'DOWN', 'pvalue': 0.0}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'groups_96', 'experimentId': 'E-MTAB-62', 'factorValue': 'lymph node', 'expression': 'UP', 'pvalue': 6.229111e-11}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'gingiva', 'expression': 'UP', 'pvalue': 0.015670406}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'groups_96', 'experimentId': 'E-MTAB-62', 'factorValue': 'cerebellum', 'expression': 'UP', 'pvalue': 0.0003318383}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'cord blood', 'expression': 'DOWN', 'pvalue': 8.6808584e-05}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'left ventricular myocardium', 'expression': 'DOWN', 'pvalue': 0.042837437}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'hypothalamus', 'expression': 'UP', 'pvalue': 2.11633e-40}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'groups_369', 'experimentId': 'E-MTAB-62', 'factorValue': 'amygdala', 'expression': 'UP', 'pvalue': 0.00092426006}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'bladder', 'expression': 'DOWN', 'pvalue': 3.5734706e-15}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'groups_369', 'experimentId': 'E-MTAB-62', 'factorValue': 'myometrium', 'expression': 'UP', 'pvalue': 5.5499697e-13}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'skeletal muscle', 'expression': 'DOWN', 'pvalue': 5.8480187e-12}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'bronchial epithelium', 'expression': 'DOWN', 'pvalue': 0.00024004691}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'groups_369', 'experimentId': 'E-MTAB-62', 'factorValue': 'prefrontal cortex', 'expression': 'UP', 'pvalue': 0.0052393237}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-62', 'factorValue': 'esophagus', 'expression': 'DOWN', 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'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-25', 'factorValue': 'brain', 'expression': 'UP', 'pvalue': 0.00017227749}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-25', 'factorValue': 'olfactory bulb', 'expression': 'UP', 'pvalue': 0.044298626}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-25', 'factorValue': 'bone marrow', 'expression': 'DOWN', 'pvalue': 0.04899348}, {'technologyPlatform': 'A-AFFY-33', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-MTAB-25', 'factorValue': 'spinal cord', 'expression': 'UP', 'pvalue': 0.03662241}, {'technologyPlatform': 'A-AFFY-44', 'geneName': 'ENSG00000162512', 'experimentalFactor': 'organism_part', 'experimentId': 'E-GEOD-13319', 'factorValue': 'myometrium', 'expression': 'DOWN', 'pvalue': 0.0010488235}, 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'OTTHUMT00000102016', 'dbName': 'vega_transcript'}, {'dbDisplayName': 'Vega transcript', 'id': 'SDC3-001', 'dbName': 'vega_transcript'}, {'dbDisplayName': 'UniProtKB/TrEMBL', 'id': 'D3DPN2', 'dbName': 'uniprotkb/trembl'}, {'dbDisplayName': 'UCSC Stable ID', 'id': 'uc001bsd.2', 'dbName': 'ucsc_stable_id'}, {'dbDisplayName': 'UCSC Stable ID', 'id': 'uc001bsd', 'dbName': 'ucsc_stable_id'}, {'dbDisplayName': 'Human Protein Atlas', 'id': 'CAB025786', 'dbName': 'human_protein_atlas'}, {'dbDisplayName': 'Human Protein Atlas', 'id': 'HPA017087', 'dbName': 'human_protein_atlas'}, {'dbDisplayName': 'European Nucleotide Archive', 'id': 'AL445235', 'dbName': 'european_nucleotide_archive'}, {'dbDisplayName': 'European Nucleotide Archive', 'id': 'CH471059', 'dbName': 'european_nucleotide_archive'}, {'dbDisplayName': 'GO', 'id': 'GO:0016021', 'dbName': 'go'}, {'dbDisplayName': 'HGNC transcript name', 'id': 'SDC3-001', 'dbName': 'hgnc_transcript_name'}, {'dbDisplayName': 'Vega translation', 'id': '139894', 'dbName': 'vega_translation'}, {'dbDisplayName': 'Vega translation', 'id': 'OTTHUMP00000040576', 'dbName': 'vega_translation'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005575', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'EAX07636.1', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'EAX07636', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'EAX07638.1', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'EAX07638', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'Havana translation', 'id': 'OTTHUMP00000040576', 'dbName': 'havana_translation'}, {'dbDisplayName': 'Havana transcript', 'id': 'OTTHUMT00000102016', 'dbName': 'havana_transcript'}, {'dbDisplayName': 'UniParc', 'id': 'UPI000013571A', 'dbName': 'uniparc'}, {'dbDisplayName': 'PrimeView', 'id': '11739277_at', 'dbName': 'primeview'}, {'dbDisplayName': 'U133_X3P', 'id': 'g7662137_3p_at', 'dbName': 'u133_x3p'}, {'dbDisplayName': 'U133_X3P', 'id': 'Hs2.158287.2.S1_3p_s_at', 'dbName': 'u133_x3p'}, {'dbDisplayName': 'HG-U133A_2', 'id': '202898_at', 'dbName': 'hg_u133a_2'}, {'dbDisplayName': 'HG-U133A', 'id': '202898_at', 'dbName': 'hg_u133a'}, {'dbDisplayName': 'HG-U133_Plus_2', 'id': '202898_at', 'dbName': 'hg_u133_plus_2'}, {'dbDisplayName': 'PrimeView', 'id': '11739276_at', 'dbName': 'primeview'}, {'dbDisplayName': 'HG-U95Av2', 'id': '32092_at', 'dbName': 'hg_u95av2'}, {'dbDisplayName': 'HG-U95A', 'id': '32092_at', 'dbName': 'hg_u95a'}, {'dbDisplayName': 'HG-U133_Plus_2', 'id': '1554864_a_at', 'dbName': 'hg_u133_plus_2'}, {'dbDisplayName': 'UniProtKB ACC', 'id': 'D3DPN2', 'dbName': 'uniprotkb_acc'}, {'dbDisplayName': 'UniProtKB ID', 'id': 'D3DPN2_HUMAN', 'dbName': 'uniprotkb_id'}], 'end': 31351587, 'name': 'SDC3-001', 'exons': [{'exonNumber': 1, 'end': 31351587, 'genomicCodingEnd': 31350094, 'sequence': 'CTGAGCCACCTCTGTGGGTCCAGGGGCAGTGGTCCCCAGGGGCAGGGTGCTCCTCTCAGGGATGTCAGGCTCCTGGGTGGTGGCCGGCCTGGGAAGGGCTCTTGGCCGGGAGGTAGCTGTGCTGACCAGCCTGGGTGTTGGGGCCTCGGTGTCCAAGACAGCCGCCGTGGTGGGCGGGGAGGGCGCCTCGGGGGTAGTGGCCCGTGCCGTAGCCACTGTGGTCAGTGGGAGAGGCAGAAGCCTCCGTACGCCAGTGGTCCTTATAACAGCAGTGGTGGCCGTAAAAGGGGGTGCTGCAGGGGTGCTGGGGGTGGCGGTGGCCACTGTGGCAGGCACTGTGGCCACAGTCGGGTCCCCTGTGCTTGTGGCAGCAGTGGTAGCCATGGTAGTGGAGACGGTGGTGGCTCTCTGGCTGGGCTCTTCCGGGACTTCTGTCACCACCAGGGGGCTGGTGGCTGGCTCCAGGGTGGGGCGCTCAGAGGGGAGCTCTTCAAATGGTGTGCCCACAGGCTGGATGTTCGTGGTGGGCAGCACCGCAGGTGTGGTGGACACCGCCAGGGCTACATCTGGGCTGAAGCGCATGGCTGTCTCAATGCCCGACTCCTGCTCGAAGTCTGAGGGGGTGGGGGAGAGGGAGAGAGCTAGGGAGCTGGGTGGTTGTGAGGGGCATGAGGATCCCAGGTAAGCAATGGCCATCAAGATTAGGTCTCCCAACCCCCTCTCTTTACCCAATTTTCCCAGAAAAGATGAGAGAAAGGAGGAAGGCACAGCCCAGCTAAAGGTGGTCAGTTGCTGATGTTCCCCAACTTCTCTCTGCCAAGTCAAAAATTCTGGGGGCCGCCTCTCCCGGGAAGCCTTCCTTGACTATTCCTGCCCACCCAGCCTACAGTTTCTATGAGGTTGAATCCAGGCAGCAGCAACTGAGGCGCTACTGGCTGCAAAACTTGCTGGGGCTTGCAGGGGAACACAGGAGTGGCATTCTGGGAAGAGTCAGACCCCAAAGGCACCCCTACCACAAGCTCAAGGCAGGGGTGGTACACTAAGGGCTTCCCCCAGAGGCAGAGGCGGAGGGTAAAAGGGAAAAGAAGCCCTTGAGGCAGGGGAACTGCTTGAGCAATCTGGCTGACGCAAAGCCGGGACAGTGAAGGAACTTGGGAGGAAATGAGATGGGGAGTAGGGGATGGGGGAGGGAGAAGCCACAGCCAGCTCCTGGGCTCGGAACCAGGCAGGAGGGAGGGGAGCCAGGGAACTTTGCGAATAGAGATGTGACCCAATATAAACGGGTTTTACAAAGATTAATTTGAAAGAGGCTCAAAGGACTTGGCTAAGGAGGGGAGACCAGAGGCGAGGGCTGTGGGGAGCCAGCTCTGTGGCGTGCAGACCCCGTACCATCTCCTCAGATGCCAGCCCGTGCCCTCACTGGGCCCAGTCTCAGCTGCCTTCTTTTTGCTACCATTTTGAGAGCTCCTCCTCTGTGCCAGACCCCAGCTTCCTATCCCAAACCCTCCTAGAGGCACTGAGAAGAAGTCGTATTTCTCACCATCCACAGGTGAAAATACAGGGATTCAGGGAGGGGGAGCACCGAGGGGCACACAGTTGCTACATGGCAGAGTGGGGTTCGCGGTGCCCTTCTCTCCCGAGATTCTGCTAGACCCAGCTGACCTGGCTCCCCTTCCCCAGGGCGGGGCCATCCCAGGCACCACTTGAAGCACCTGCCCTGTGTCATCACTGCCCTAACCCCACCATTGGCCACAGCTTATTGCACCTGACGGGACCACCGGAACCAAGCAAGGTCTGCAGAGAAAGCCACATAGCACACACAAAGATGCAGACGTGGGACCCTGGAGACCTGGACATTCTGGGCCCTGAGGTCCTCCCAGGTCTTGTTCTATCCCCAGAAGGATGTTCTGCCCTTCTTGTTCTGGGGATCCAGAGCAAGAAGAACTTGCCTGACCCAGGCAGTGAATGCCCCCTGCCTCACTGAAGCAAGCCCCCCGTGGGCTTCTCAGAGTTGAGGCTGGATACAGACTGGTCACTGCCCCCAGGCAGAGGTAGGGAGGGGGGTACTTACAGCCCGAGCCCGACCCCGAGTAGAGGTCATCCAGTTCATCATCGGGAAAGGAGTCATCATCCCCAGAGCCCTCCAGGTCCACGGGTCTCTCGAAGTTCTCACTGCGCCAGCGCTGGGC', 'cdsEnd': 696, 'cdnaCodingEnd': 2189, 'start': 31349399, 'phase': 0, 'strand': '-', 'genomicCodingStart': 31349399, 'cdnaCodingStart': 1494, 'cdsStart': 1, 'id': 'ENSE00001909382', 'chromosome': '1'}, {'exonNumber': 2, 'end': 31347435, 'genomicCodingEnd': 31347435, 'sequence': 'CTACGAGCACCTCCTTCCGCTCCAGGATACTCTTCTGAGGCAGCTGAGCAGCTGAGCTGCCCGAGTCGATGGCATTGTCCAGGAGGCCAGGGCCCGGGCGGGCACCCTTGGGCAGTGTCCCAGGTGGAGATGATGCCTTGGCCGCAGCCCCTCCCACAGCTACCACCTCATTGGCTGTGTCTGGTTGTGTGGTCTCTTCTTCTGGCAGCTCGAAGTCTCCACTGGGCCCCCCACTCACCGGAACCTCTGGCTCATCCCGGATTGTGGTCAGGAAGGTCTCTGGAGTTGGGGT', 'cdsEnd': 988, 'cdnaCodingEnd': 2481, 'start': 31347144, 'phase': 0, 'strand': '-', 'genomicCodingStart': 31347144, 'cdnaCodingStart': 2190, 'cdsStart': 697, 'id': 'ENSE00001065952', 'chromosome': '1'}, {'exonNumber': 3, 'end': 31346224, 'genomicCodingEnd': 31346224, 'sequence': 'CATTTCAGCTTAATTTTATTTCCTCTTATAAATGGGCACAGCACAGGAAGTGTTAAAAAAACAAACAAACAAAAAAAAAAAAAAAAAAAAAAAAACAAAAACAAAACCAGTTCCTTCACAAGGCTGGAACAGGAGAGTACCCGCAGTGGGGCAGGCGCCTTGGTCTCTTTTTTCCACTGTCTTTTTCTTTTGTTTTTCTTATTTAAGGTTTTGGCCATGAACTCAGGACAGGTATGGTTAATAAACAGGTTACAGGGGAGAGAAGGGGCAGGGAAGGCCTGGGGGAGGGAATGGCAGACCCCCACCCACCCCAGGCAGGTTCTGTACAGGAGAAAGGACTCACAGGAGGGAGGGACACTGTCTTCAGGGGGCTCTCTGGAGCCACGCTGCCTACGAAAAATATTTACATGCATTTGCCACGCTGAGGCCAGGGTCACTGTGGTGCCAGGCAGGCACCTGGGGGATGCTGGGGCCATCGGCTCTCAGATGGCAACTCCCAGGGCCCAGTCTCGATGCCTCTGTAAATCTGTACAGTTTGCGGGCTTCTATTTACAGGCAAGAGGCCTGGGGAGGCAAGTCCAGGGTTGTAGTTGTTGGGAGAAGAAATCCAGAGAACACAGGAGGCAGCCACTCCTACCCCATGAGGCAGAGGGTCTGCTCCCTGTGTCCAGGGGCCCCCACCAGGAGGCCTGACAGGCGGCTTTGCCAACCCCAGGGGGGTTTGGCCCACACACCCTAAGCCCTGCCCAGCCCTGGTTGCCACCCACATGCCTCCAGCGATCAAGGGGACCAGTCTTTCAGGCAAGGCCCCCATCTGGCCTCCTGGCCTCCTGGAGACAGGGTCTGGGCTCTCCAGGTCCTGGCCTGCCTCGTGCTCTGGCAGCCAAGGCCCCAGAGGCTCTCAAGCCACAGAAGCTCCCTCTCATTTGGAACTCCCTGTGCTTCCAGCAAATGCCAAAGCCCCTCAGAACACTCCATCACAGGCAGGGGTAGGGGGACATGAGGGCCCTGCACCCACATTGCACCTGGGAGAGCCTAGCTGGTCCTCACTGAACTCTCTTGGACTGCCTTGCCCCGGTCAGGCCGGCCAGGGCAGATTTGGGCTGGTCAGACTCCTCATCCTCAGGAGGATAAAGCCTGGACATCTGCCTTGGGTCCAGGGATCCATGAACAAGGCCCCTGGCCTCTTCTCTCAAATGCTAAGGACACAGAGAAGAGAAGCCAGTGCCTGGAGCCCAAGCCCCAAATCAGAAGCCAACCCCTGGGATGTGAGGAGCCAGGCCTGCCGGGGCCACCCCCACCATTGGCTCCAGCCCTACTGAGAAACTGCACCCACTGTTGGGTCTCCCACCTGGGGTCCAGCATCTTCTGGGGCTGGGGGCCCAAGCCCTTTTCTCCTCTATCCTCCCTGGTTTCTCAGCCTCGGCCTGCCCAGGCCGTCTCACCAGAGCTGTGCTCTCCAAGACAGCAGCACCCCAGGGAGCAGGGTAGGGAGGCTGAGCCTTGTGGTCTGTGGCCCCAGGACCCAGCCCTTCTGCTCCAAAGATGACTGAGGCCAACCCGCCCCCTCCAGATATCAGGGGCCCCCCATGCCCACTCTTCTAAGGCTGGGTCCACCTGGCTTCCTCACAAGCCTCTGGGCCCTGTGAAGGAGGGTTTTGGGACTGGAAGATGGAGCCCAGCCTGGAAAAGACAGGCTGTGGGACAGCCCCTGGAACCTCCCCCTCACTGCCTACACACCGCTACCCCTCATCCTGCAGAAATCTGCTGCCAGGGCATCTTGAAAAGGGCCCTGAAATAAAACCTGCCTTCCTGACTTGAATCTGGGATGTGGGTGAGGGGTGGGGGTGTGAGTGCCAGCCAATCGCAACTCACACCACATCCCTTTGGCTCCAAGAGGCCCCCTGCCAAGCACACCCTCCCCAAAAGATCTGTGACCCCACATTTAAAATACCGATGGAAATAGCCCTACTTGCTAGGTAACAAAGGAAGTAACCCCTCCCCCACTATCACCTGGTCTCATCCCTCAAACCCTGACCTCGGGGCCTGAGGGATCTGCAGGGGCTGCTTCCAGCCATGGCCCCTGAAGCTGCAGCCAGAATTGTTTGGCCAAATAGGTGAGGGGGTGTCCACAGGGAGGGCCTCTGGGCAGGTGGGCTGAGGTTGGCCTGCCAGGCAGAGGGCAGAGGGTGCGGAGGGCCCGCCCTCACAGGCACTTTGGAGACTTGTGTCCTGGGAGGCAGAGTCAGCCCCCTAGCTCAAAGCAGGAAGGGGACACAGGGAGATAAAGGAGCCCAACCACATGCCCCCTCCCTGCCCTGGGCCTTCCGTCCTGGGAGACCCAAGACCCCCCAACAACCTGGGGCCAAATTTCCTTCCTCAGCCTTAGAGGAGCCCCCAGGCTCCCAGCTAGTGGGGGTCTGGCCCCAAACCTCCCCCTCTGCCAGCTGCGGTGGGGAGGAAGCAGGTAGGGGTGAAGCCAGGCCCACCTGCATGCAATGCCCTAAAAGGGCTGTGGCCCCACACTTTTTCCGAGAAAGGCAAGGGCCTGCCTGTTTCCCTCCAGCATTGAGAGCAGGTCATGTGGAGTGAGACTGTGCATCCACATGGGATTGTGTCTGACACTGGCTGGGGTTGGCGGCTGCATGGTTGGTGTGGGCACCATGGCATGGGACTGAGTATGACGGGGCAACTTAGGGGGACCCAATATGGGCTGATTGTTCTGGCTCGATTCCACCCTCCCCAGTAAGCCTGAAAGCTGGAGACAATGTGTGTGGTGCCAGAGTGTGGGTGTATTTGGGGTAGGAGGAGGCCACACTGTCACTGTCATGTGACCATGACTAGTGACTTGCATTGCAGTACGTGTCTGGGGGTGTGTAAGTGATGCATGAGGATAAACATTCTTGGAAGGACGCGTGTGTTCTGTGATATGTCTTGATTGGCTGGGCGGTCAGGATTGCGTATGGTTTTGTCATTGCATGCTTTTGTCTTGTGTGTGACTGAGTGAAAATATGGTGATAGTGTGGGCAATGGTGTCTGTGCAGAGTCCCCTCATAGGAGGGACATCAGAGCAGCCCCTCCTCACCAGTGGCTGCCCCAGCACCCTCAGGAAGCTGTTTCTTGGGGGAAGATGCAGAAAGAAATGAAGTCTGGGTACATGTGTACTTGGCAGGCAAGAGGAGAGATTCAACAACCCCAGAGAGACCAGGACAAAACAGGCTGGTGACAAGGGACACCCTCTCACCCAGCTAGAGAGAGGCCCTGGGATACGAGCAAGAGGTTGCAGTGTCTAGATGATTTCAAGGGCTGTGTTTACCAAATGTTTGTCCTGGAAACCAGCCTGAGTGCCTCTCTGCCCCAAAAAGGAGATCTCAGTGAGCACTGTGGGTGCCAAGTCAGGGCTCAGGCTCATCTCAAGCCCCACCCTTTCTTCCACCACCAGCCAATCAGGAGCTTTCTTCCTCCCATCCATCTGACATGAGGTCCTGAAGCCCCAGACTGGTGGCAGGGATGAGGGGAACAAGAGATGAGCTCGTAAGGGCACAGTCTGGGGCAGATGGCAGCAGCCCCTCTTCCTCGGGGAAGATCTGTGTGAGGCTGGCAGCCTGGGCAGACCTTGGGAGAGAGGGCAGAGAAGAACTGGGGCCAGGTTCCAGGCCCAGTCCCAGGCTTGGGCTGGTGGGGCCAGGCTGGGGACTGGACAGCAGGGTGGTGTTGAGGCTGCAGGGAGGCACTGTGGCTCCACTAGGCATAGAACTCCTCCTGCTTGTCAGGCTTCTGGTATGTGACGCTCGCCTGCTTGGGTTCCTCCAGCGTGTAGCTGCCCTCATCCTTTTTCTTCATACGATAGATGAGCAGTGTGACCAAGAAGGCAGCAAAGAGGGCGCCCACCACCCCGCCCACAATCACAG', 'cdsEnd': 1155, 'cdnaCodingEnd': 2648, 'start': 31342314, 'phase': 2, 'strand': '-', 'genomicCodingStart': 31346058, 'cdnaCodingStart': 2482, 'cdsStart': 989, 'id': 'ENSE00001857328', 'chromosome': '1'}], 'genomicCodingEnd': 31350094, 'cDnaSequence': 'GCCCAGCGCTGGCGCAGTGAGAACTTCGAGAGACCCGTGGACCTGGAGGGCTCTGGGGATGATGACTCCTTTCCCGATGATGAACTGGATGACCTCTACTCGGGGTCGGGCTCGGGCTGTAAGTACCCCCCTCCCTACCTCTGCCTGGGGGCAGTGACCAGTCTGTATCCAGCCTCAACTCTGAGAAGCCCACGGGGGGCTTGCTTCAGTGAGGCAGGGGGCATTCACTGCCTGGGTCAGGCAAGTTCTTCTTGCTCTGGATCCCCAGAACAAGAAGGGCAGAACATCCTTCTGGGGATAGAACAAGACCTGGGAGGACCTCAGGGCCCAGAATGTCCAGGTCTCCAGGGTCCCACGTCTGCATCTTTGTGTGTGCTATGTGGCTTTCTCTGCAGACCTTGCTTGGTTCCGGTGGTCCCGTCAGGTGCAATAAGCTGTGGCCAATGGTGGGGTTAGGGCAGTGATGACACAGGGCAGGTGCTTCAAGTGGTGCCTGGGATGGCCCCGCCCTGGGGAAGGGGAGCCAGGTCAGCTGGGTCTAGCAGAATCTCGGGAGAGAAGGGCACCGCGAACCCCACTCTGCCATGTAGCAACTGTGTGCCCCTCGGTGCTCCCCCTCCCTGAATCCCTGTATTTTCACCTGTGGATGGTGAGAAATACGACTTCTTCTCAGTGCCTCTAGGAGGGTTTGGGATAGGAAGCTGGGGTCTGGCACAGAGGAGGAGCTCTCAAAATGGTAGCAAAAAGAAGGCAGCTGAGACTGGGCCCAGTGAGGGCACGGGCTGGCATCTGAGGAGATGGTACGGGGTCTGCACGCCACAGAGCTGGCTCCCCACAGCCCTCGCCTCTGGTCTCCCCTCCTTAGCCAAGTCCTTTGAGCCTCTTTCAAATTAATCTTTGTAAAACCCGTTTATATTGGGTCACATCTCTATTCGCAAAGTTCCCTGGCTCCCCTCCCTCCTGCCTGGTTCCGAGCCCAGGAGCTGGCTGTGGCTTCTCCCTCCCCCATCCCCTACTCCCCATCTCATTTCCTCCCAAGTTCCTTCACTGTCCCGGCTTTGCGTCAGCCAGATTGCTCAAGCAGTTCCCCTGCCTCAAGGGCTTCTTTTCCCTTTTACCCTCCGCCTCTGCCTCTGGGGGAAGCCCTTAGTGTACCACCCCTGCCTTGAGCTTGTGGTAGGGGTGCCTTTGGGGTCTGACTCTTCCCAGAATGCCACTCCTGTGTTCCCCTGCAAGCCCCAGCAAGTTTTGCAGCCAGTAGCGCCTCAGTTGCTGCTGCCTGGATTCAACCTCATAGAAACTGTAGGCTGGGTGGGCAGGAATAGTCAAGGAAGGCTTCCCGGGAGAGGCGGCCCCCAGAATTTTTGACTTGGCAGAGAGAAGTTGGGGAACATCAGCAACTGACCACCTTTAGCTGGGCTGTGCCTTCCTCCTTTCTCTCATCTTTTCTGGGAAAATTGGGTAAAGAGAGGGGGTTGGGAGACCTAATCTTGATGGCCATTGCTTACCTGGGATCCTCATGCCCCTCACAACCACCCAGCTCCCTAGCTCTCTCCCTCTCCCCCACCCCCTCAGACTTCGAGCAGGAGTCGGGCATTGAGACAGCCATGCGCTTCAGCCCAGATGTAGCCCTGGCGGTGTCCACCACACCTGCGGTGCTGCCCACCACGAACATCCAGCCTGTGGGCACACCATTTGAAGAGCTCCCCTCTGAGCGCCCCACCCTGGAGCCAGCCACCAGCCCCCTGGTGGTGACAGAAGTCCCGGAAGAGCCCAGCCAGAGAGCCACCACCGTCTCCACTACCATGGCTACCACTGCTGCCACAAGCACAGGGGACCCGACTGTGGCCACAGTGCCTGCCACAGTGGCCACCGCCACCCCCAGCACCCCTGCAGCACCCCCTTTTACGGCCACCACTGCTGTTATAAGGACCACTGGCGTACGGAGGCTTCTGCCTCTCCCACTGACCACAGTGGCTACGGCACGGGCCACTACCCCCGAGGCGCCCTCCCCGCCCACCACGGCGGCTGTCTTGGACACCGAGGCCCCAACACCCAGGCTGGTCAGCACAGCTACCTCCCGGCCAAGAGCCCTTCCCAGGCCGGCCACCACCCAGGAGCCTGACATCCCTGAGAGGAGCACCCTGCCCCTGGGGACCACTGCCCCTGGACCCACAGAGGTGGCTCAGACCCCAACTCCAGAGACCTTCCTGACCACAATCCGGGATGAGCCAGAGGTTCCGGTGAGTGGGGGGCCCAGTGGAGACTTCGAGCTGCCAGAAGAAGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTGTGGGAGGGGCTGCGGCCAAGGCATCATCTCCACCTGGGACACTGCCCAAGGGTGCCCGCCCGGGCCCTGGCCTCCTGGACAATGCCATCGACTCGGGCAGCTCAGCTGCTCAGCTGCCTCAGAAGAGTATCCTGGAGCGGAAGGAGGTGCTCGTAGCTGTGATTGTGGGCGGGGTGGTGGGCGCCCTCTTTGCTGCCTTCTTGGTCACACTGCTCATCTATCGTATGAAGAAAAAGGATGAGGGCAGCTACACGCTGGAGGAACCCAAGCAGGCGAGCGTCACATACCAGAAGCCTGACAAGCAGGAGGAGTTCTATGCCTAGTGGAGCCACAGTGCCTCCCTGCAGCCTCAACACCACCCTGCTGTCCAGTCCCCAGCCTGGCCCCACCAGCCCAAGCCTGGGACTGGGCCTGGAACCTGGCCCCAGTTCTTCTCTGCCCTCTCTCCCAAGGTCTGCCCAGGCTGCCAGCCTCACACAGATCTTCCCCGAGGAAGAGGGGCTGCTGCCATCTGCCCCAGACTGTGCCCTTACGAGCTCATCTCTTGTTCCCCTCATCCCTGCCACCAGTCTGGGGCTTCAGGACCTCATGTCAGATGGATGGGAGGAAGAAAGCTCCTGATTGGCTGGTGGTGGAAGAAAGGGTGGGGCTTGAGATGAGCCTGAGCCCTGACTTGGCACCCACAGTGCTCACTGAGATCTCCTTTTTGGGGCAGAGAGGCACTCAGGCTGGTTTCCAGGACAAACATTTGGTAAACACAGCCCTTGAAATCATCTAGACACTGCAACCTCTTGCTCGTATCCCAGGGCCTCTCTCTAGCTGGGTGAGAGGGTGTCCCTTGTCACCAGCCTGTTTTGTCCTGGTCTCTCTGGGGTTGTTGAATCTCTCCTCTTGCCTGCCAAGTACACATGTACCCAGACTTCATTTCTTTCTGCATCTTCCCCCAAGAAACAGCTTCCTGAGGGTGCTGGGGCAGCCACTGGTGAGGAGGGGCTGCTCTGATGTCCCTCCTATGAGGGGACTCTGCACAGACACCATTGCCCACACTATCACCATATTTTCACTCAGTCACACACAAGACAAAAGCATGCAATGACAAAACCATACGCAATCCTGACCGCCCAGCCAATCAAGACATATCACAGAACACACGCGTCCTTCCAAGAATGTTTATCCTCATGCATCACTTACACACCCCCAGACACGTACTGCAATGCAAGTCACTAGTCATGGTCACATGACAGTGACAGTGTGGCCTCCTCCTACCCCAAATACACCCACACTCTGGCACCACACACATTGTCTCCAGCTTTCAGGCTTACTGGGGAGGGTGGAATCGAGCCAGAACAATCAGCCCATATTGGGTCCCCCTAAGTTGCCCCGTCATACTCAGTCCCATGCCATGGTGCCCACACCAACCATGCAGCCGCCAACCCCAGCCAGTGTCAGACACAATCCCATGTGGATGCACAGTCTCACTCCACATGACCTGCTCTCAATGCTGGAGGGAAACAGGCAGGCCCTTGCCTTTCTCGGAAAAAGTGTGGGGCCACAGCCCTTTTAGGGCATTGCATGCAGGTGGGCCTGGCTTCACCCCTACCTGCTTCCTCCCCACCGCAGCTGGCAGAGGGGGAGGTTTGGGGCCAGACCCCCACTAGCTGGGAGCCTGGGGGCTCCTCTAAGGCTGAGGAAGGAAATTTGGCCCCAGGTTGTTGGGGGGTCTTGGGTCTCCCAGGACGGAAGGCCCAGGGCAGGGAGGGGGCATGTGGTTGGGCTCCTTTATCTCCCTGTGTCCCCTTCCTGCTTTGAGCTAGGGGGCTGACTCTGCCTCCCAGGACACAAGTCTCCAAAGTGCCTGTGAGGGCGGGCCCTCCGCACCCTCTGCCCTCTGCCTGGCAGGCCAACCTCAGCCCACCTGCCCAGAGGCCCTCCCTGTGGACACCCCCTCACCTATTTGGCCAAACAATTCTGGCTGCAGCTTCAGGGGCCATGGCTGGAAGCAGCCCCTGCAGATCCCTCAGGCCCCGAGGTCAGGGTTTGAGGGATGAGACCAGGTGATAGTGGGGGAGGGGTTACTTCCTTTGTTACCTAGCAAGTAGGGCTATTTCCATCGGTATTTTAAATGTGGGGTCACAGATCTTTTGGGGAGGGTGTGCTTGGCAGGGGGCCTCTTGGAGCCAAAGGGATGTGGTGTGAGTTGCGATTGGCTGGCACTCACACCCCCACCCCTCACCCACATCCCAGATTCAAGTCAGGAAGGCAGGTTTTATTTCAGGGCCCTTTTCAAGATGCCCTGGCAGCAGATTTCTGCAGGATGAGGGGTAGCGGTGTGTAGGCAGTGAGGGGGAGGTTCCAGGGGCTGTCCCACAGCCTGTCTTTTCCAGGCTGGGCTCCATCTTCCAGTCCCAAAACCCTCCTTCACAGGGCCCAGAGGCTTGTGAGGAAGCCAGGTGGACCCAGCCTTAGAAGAGTGGGCATGGGGGGCCCCTGATATCTGGAGGGGGCGGGTTGGCCTCAGTCATCTTTGGAGCAGAAGGGCTGGGTCCTGGGGCCACAGACCACAAGGCTCAGCCTCCCTACCCTGCTCCCTGGGGTGCTGCTGTCTTGGAGAGCACAGCTCTGGTGAGACGGCCTGGGCAGGCCGAGGCTGAGAAACCAGGGAGGATAGAGGAGAAAAGGGCTTGGGCCCCCAGCCCCAGAAGATGCTGGACCCCAGGTGGGAGACCCAACAGTGGGTGCAGTTTCTCAGTAGGGCTGGAGCCAATGGTGGGGGTGGCCCCGGCAGGCCTGGCTCCTCACATCCCAGGGGTTGGCTTCTGATTTGGGGCTTGGGCTCCAGGCACTGGCTTCTCTTCTCTGTGTCCTTAGCATTTGAGAGAAGAGGCCAGGGGCCTTGTTCATGGATCCCTGGACCCAAGGCAGATGTCCAGGCTTTATCCTCCTGAGGATGAGGAGTCTGACCAGCCCAAATCTGCCCTGGCCGGCCTGACCGGGGCAAGGCAGTCCAAGAGAGTTCAGTGAGGACCAGCTAGGCTCTCCCAGGTGCAATGTGGGTGCAGGGCCCTCATGTCCCCCTACCCCTGCCTGTGATGGAGTGTTCTGAGGGGCTTTGGCATTTGCTGGAAGCACAGGGAGTTCCAAATGAGAGGGAGCTTCTGTGGCTTGAGAGCCTCTGGGGCCTTGGCTGCCAGAGCACGAGGCAGGCCAGGACCTGGAGAGCCCAGACCCTGTCTCCAGGAGGCCAGGAGGCCAGATGGGGGCCTTGCCTGAAAGACTGGTCCCCTTGATCGCTGGAGGCATGTGGGTGGCAACCAGGGCTGGGCAGGGCTTAGGGTGTGTGGGCCAAACCCCCCTGGGGTTGGCAAAGCCGCCTGTCAGGCCTCCTGGTGGGGGCCCCTGGACACAGGGAGCAGACCCTCTGCCTCATGGGGTAGGAGTGGCTGCCTCCTGTGTTCTCTGGATTTCTTCTCCCAACAACTACAACCCTGGACTTGCCTCCCCAGGCCTCTTGCCTGTAAATAGAAGCCCGCAAACTGTACAGATTTACAGAGGCATCGAGACTGGGCCCTGGGAGTTGCCATCTGAGAGCCGATGGCCCCAGCATCCCCCAGGTGCCTGCCTGGCACCACAGTGACCCTGGCCTCAGCGTGGCAAATGCATGTAAATATTTTTCGTAGGCAGCGTGGCTCCAGAGAGCCCCCTGAAGACAGTGTCCCTCCCTCCTGTGAGTCCTTTCTCCTGTACAGAACCTGCCTGGGGTGGGTGGGGGTCTGCCATTCCCTCCCCCAGGCCTTCCCTGCCCCTTCTCTCCCCTGTAACCTGTTTATTAACCATACCTGTCCTGAGTTCATGGCCAAAACCTTAAATAAGAAAAACAAAAGAAAAAGACAGTGGAAAAAAGAGACCAAGGCGCCTGCCCCACTGCGGGTACTCTCCTGTTCCAGCCTTGTGAAGGAACTGGTTTTGTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTGTTTGTTTGTTTTTTTAACACTTCCTGTGCTGTGCCCATTTATAAGAGGAAATAAAATTAAGCTGAAATG', 'proteinID': 'ENSP00000338346', 'strand': '-', 'cdnaCodingEnd': 2648, 'start': 31342314, 'biotype': 'protein_coding', 'genomicCodingStart': 31346058, 'cdnaCodingStart': 1494, 'cdsLength': 1154, 'id': 'ENST00000336798', 'chromosome': '1', 'proteinSequence': 'MAIAYLGSSCPSQPPSSLALSLSPTPSDFEQESGIETAMRFSPDVALAVSTTPAVLPTTNIQPVGTPFEELPSERPTLEPATSPLVVTEVPEEPSQRATTVSTTMATTAATSTGDPTVATVPATVATATPSTPAAPPFTATTAVIRTTGVRRLLPLPLTTVATARATTPEAPSPPTTAAVLDTEAPTPRLVSTATSRPRALPRPATTQEPDIPERSTLPLGTTAPGPTEVAQTPTPETFLTTIRDEPEVPVSGGPSGDFELPEEETTQPDTANEVVAVGGAAAKASSPPGTLPKGARPGPGLLDNAIDSGSSAAQLPQKSILERKEVLVAVIVGGVVGALFAAFLVTLLIYRMKKKDEGSYTLEEPKQASVTYQKPDKQEEFYA'}, {'status': 'KNOWN', 'xrefs': [{'dbDisplayName': 'Ensembl gene', 'id': 'ENSG00000162512', 'dbName': 'ensembl_gene'}, {'dbDisplayName': 'Vega gene', 'id': 'SDC3', 'dbName': 'vega_gene'}, {'dbDisplayName': 'Ensembl transcript', 'id': 'ENST00000339394', 'dbName': 'ensembl_transcript'}, {'dbDisplayName': 'Ensembl protein', 'id': 'ENSP00000344468', 'dbName': 'ensembl_protein'}, {'dbDisplayName': 'InterPro', 'id': 'IPR003585', 'dbName': 'interpro'}, {'dbDisplayName': 'InterPro', 'id': 'IPR027789', 'dbName': 'interpro'}, {'dbDisplayName': 'CCDS', 'id': 'CCDS30661.1', 'dbName': 'ccds'}, {'dbDisplayName': 'CCDS', 'id': 'CCDS30661', 'dbName': 'ccds'}, {'dbDisplayName': 'UniProtKB/Swiss-Prot', 'id': 'O75056', 'dbName': 'uniprotkb/swissprot'}, {'dbDisplayName': 'RefSeq peptide', 'id': 'NP_055469.3', 'dbName': 'refseq_peptide'}, {'dbDisplayName': 'RefSeq peptide', 'id': 'NP_055469', 'dbName': 'refseq_peptide'}, {'dbDisplayName': 'RefSeq mRNA', 'id': 'NM_014654.3', 'dbName': 'refseq_mrna'}, {'dbDisplayName': 'RefSeq mRNA', 'id': 'NM_014654', 'dbName': 'refseq_mrna'}, {'dbDisplayName': 'Vega transcript', 'id': 'OTTHUMT00000102017', 'dbName': 'vega_transcript'}, {'dbDisplayName': 'Vega transcript', 'id': 'SDC3-002', 'dbName': 'vega_transcript'}, {'dbDisplayName': 'UCSC Stable ID', 'id': 'uc001bse.2', 'dbName': 'ucsc_stable_id'}, {'dbDisplayName': 'UCSC Stable ID', 'id': 'uc001bse', 'dbName': 'ucsc_stable_id'}, {'dbDisplayName': 'Human Protein Atlas', 'id': 'CAB025786', 'dbName': 'human_protein_atlas'}, {'dbDisplayName': 'Human Protein Atlas', 'id': 'CAB025786', 'dbName': 'human_protein_atlas'}, {'dbDisplayName': 'Human Protein Atlas', 'id': 'HPA017087', 'dbName': 'human_protein_atlas'}, {'dbDisplayName': 'Human Protein Atlas', 'id': 'HPA017087', 'dbName': 'human_protein_atlas'}, {'dbDisplayName': 'Human Protein Atlas', 'id': 'HPA048085', 'dbName': 'human_protein_atlas'}, {'dbDisplayName': 'European Nucleotide Archive', 'id': 'AB007937', 'dbName': 'european_nucleotide_archive'}, {'dbDisplayName': 'European Nucleotide Archive', 'id': 'AF248634', 'dbName': 'european_nucleotide_archive'}, {'dbDisplayName': 'European Nucleotide Archive', 'id': 'AL445235', 'dbName': 'european_nucleotide_archive'}, {'dbDisplayName': 'European Nucleotide Archive', 'id': 'BC013974', 'dbName': 'european_nucleotide_archive'}, {'dbDisplayName': 'GO', 'id': 'GO:0001523', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0005796', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0005886', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0005975', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0006024', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0006027', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0007603', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0009405', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0016020', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0016021', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0030198', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0030203', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0030204', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0043202', 'dbName': 'go'}, {'dbDisplayName': 'GO', 'id': 'GO:0044281', 'dbName': 'go'}, {'dbDisplayName': 'HGNC transcript name', 'id': 'SDC3-002', 'dbName': 'hgnc_transcript_name'}, {'dbDisplayName': 'Vega translation', 'id': '139895', 'dbName': 'vega_translation'}, {'dbDisplayName': 'Vega translation', 'id': 'OTTHUMP00000040577', 'dbName': 'vega_translation'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005575', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005622', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005623', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005737', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005764', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005773', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005794', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005886', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0005975', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0006629', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0006790', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0007165', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0008150', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0009056', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0009058', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0030198', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0043226', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'GOSlim GOA', 'id': 'GO:0044281', 'dbName': 'goslim_goa'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'AAK39969.1', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'AAK39969', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'BAA32313.2', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'BAA32313', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'CAI22245.1', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'CAI22245', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'CAI22250.1', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'INSDC protein ID', 'id': 'CAI22250', 'dbName': 'insdc_protein_id'}, {'dbDisplayName': 'Havana translation', 'id': 'OTTHUMP00000040577', 'dbName': 'havana_translation'}, {'dbDisplayName': 'Havana transcript', 'id': 'OTTHUMT00000102017', 'dbName': 'havana_transcript'}, {'dbDisplayName': 'UniParc', 'id': 'UPI000045619B', 'dbName': 'uniparc'}, {'dbDisplayName': 'U133_X3P', 'id': 'Hs2.158287.2.S1_3p_s_at', 'dbName': 'u133_x3p'}, {'dbDisplayName': 'PrimeView', 'id': '11739276_at', 'dbName': 'primeview'}, {'dbDisplayName': 'HG-U133_Plus_2', 'id': '1554864_a_at', 'dbName': 'hg_u133_plus_2'}, {'dbDisplayName': 'UniProtKB ACC', 'id': 'O75056', 'dbName': 'uniprotkb_acc'}, {'dbDisplayName': 'UniProtKB ID', 'id': 'SDC3_HUMAN', 'dbName': 'uniprotkb_id'}], 'end': 31381608, 'name': 'SDC3-002', 'exons': [{'exonNumber': 1, 'end': 31381608, 'genomicCodingEnd': 31381433, 'sequence': 'CCCCGCGGCGCGCCCCGCCAGCAGCAGCAGCAGCAGCGGTGGCAGGAGCAGCCCGCGGGCCCCGGGCCCGGCCGCGGCCCCGGCCCCGGCGCCGGCCCCGTGGGCGGCCCCGGCACGGTGCGGCGGCCCCGGCTTCATGGCGGCGGCGCGGGCGCGGGCGGCGGGCGGCGGGCGGGCGCCTTTGTTCCCGAGGCGCGGCGCGCGGGGCGGCTGCTTGGCGGCGGCGCGGCCCGGCGGCTGGACCGACGCGCTCTAGGCTCGCGGGCTCCCGGCTCGGCCGCCCGGCTCCGCCTCGCAGCTCCGCGCCCACAGC', 'cdsEnd': 138, 'cdnaCodingEnd': 313, 'start': 31381296, 'phase': 0, 'strand': '-', 'genomicCodingStart': 31381296, 'cdnaCodingStart': 176, 'cdsStart': 1, 'id': 'ENSE00001461463', 'chromosome': '1'}, {'exonNumber': 2, 'end': 31351587, 'genomicCodingEnd': 31351587, 'sequence': 'AGCCCGAGCCCGACCCCGAGTAGAGGTCATCCAGTTCATCATCGGGAAAGGAGTCATCATCCCCAGAGCCCTCCAGGTCCACGGGTCTCTCGAAGTTCTCACTGCGCCAGCGCTGGGC', 'cdsEnd': 256, 'cdnaCodingEnd': 431, 'start': 31351470, 'phase': 0, 'strand': '-', 'genomicCodingStart': 31351470, 'cdnaCodingStart': 314, 'cdsStart': 139, 'id': 'ENSE00003606923', 'chromosome': '1'}, {'exonNumber': 3, 'end': 31350012, 'genomicCodingEnd': 31350012, 'sequence': 'CTGAGCCACCTCTGTGGGTCCAGGGGCAGTGGTCCCCAGGGGCAGGGTGCTCCTCTCAGGGATGTCAGGCTCCTGGGTGGTGGCCGGCCTGGGAAGGGCTCTTGGCCGGGAGGTAGCTGTGCTGACCAGCCTGGGTGTTGGGGCCTCGGTGTCCAAGACAGCCGCCGTGGTGGGCGGGGAGGGCGCCTCGGGGGTAGTGGCCCGTGCCGTAGCCACTGTGGTCAGTGGGAGAGGCAGAAGCCTCCGTACGCCAGTGGTCCTTATAACAGCAGTGGTGGCCGTAAAAGGGGGTGCTGCAGGGGTGCTGGGGGTGGCGGTGGCCACTGTGGCAGGCACTGTGGCCACAGTCGGGTCCCCTGTGCTTGTGGCAGCAGTGGTAGCCATGGTAGTGGAGACGGTGGTGGCTCTCTGGCTGGGCTCTTCCGGGACTTCTGTCACCACCAGGGGGCTGGTGGCTGGCTCCAGGGTGGGGCGCTCAGAGGGGAGCTCTTCAAATGGTGTGCCCACAGGCTGGATGTTCGTGGTGGGCAGCACCGCAGGTGTGGTGGACACCGCCAGGGCTACATCTGGGCTGAAGCGCATGGCTGTCTCAATGCCCGACTCCTGCTCGAAGT', 'cdsEnd': 870, 'cdnaCodingEnd': 1045, 'start': 31349399, 'phase': 2, 'strand': '-', 'genomicCodingStart': 31349399, 'cdnaCodingStart': 432, 'cdsStart': 257, 'id': 'ENSE00001399392', 'chromosome': '1'}, {'exonNumber': 4, 'end': 31347435, 'genomicCodingEnd': 31347435, 'sequence': 'CTACGAGCACCTCCTTCCGCTCCAGGATACTCTTCTGAGGCAGCTGAGCAGCTGAGCTGCCCGAGTCGATGGCATTGTCCAGGAGGCCAGGGCCCGGGCGGGCACCCTTGGGCAGTGTCCCAGGTGGAGATGATGCCTTGGCCGCAGCCCCTCCCACAGCTACCACCTCATTGGCTGTGTCTGGTTGTGTGGTCTCTTCTTCTGGCAGCTCGAAGTCTCCACTGGGCCCCCCACTCACCGGAACCTCTGGCTCATCCCGGATTGTGGTCAGGAAGGTCTCTGGAGTTGGGGT', 'cdsEnd': 1162, 'cdnaCodingEnd': 1337, 'start': 31347144, 'phase': 0, 'strand': '-', 'genomicCodingStart': 31347144, 'cdnaCodingStart': 1046, 'cdsStart': 871, 'id': 'ENSE00001065952', 'chromosome': '1'}, {'exonNumber': 5, 'end': 31346224, 'genomicCodingEnd': 31346224, 'sequence': 'GCTTGGGCTGGTGGGGCCAGGCTGGGGACTGGACAGCAGGGTGGTGTTGAGGCTGCAGGGAGGCACTGTGGCTCCACTAGGCATAGAACTCCTCCTGCTTGTCAGGCTTCTGGTATGTGACGCTCGCCTGCTTGGGTTCCTCCAGCGTGTAGCTGCCCTCATCCTTTTTCTTCATACGATAGATGAGCAGTGTGACCAAGAAGGCAGCAAAGAGGGCGCCCACCACCCCGCCCACAATCACAG', 'cdsEnd': 1329, 'cdnaCodingEnd': 1504, 'start': 31345982, 'phase': 2, 'strand': '-', 'genomicCodingStart': 31346058, 'cdnaCodingStart': 1338, 'cdsStart': 1163, 'id': 'ENSE00001952023', 'chromosome': '1'}], 'genomicCodingEnd': 31381433, 'cDnaSequence': 'GCTGTGGGCGCGGAGCTGCGAGGCGGAGCCGGGCGGCCGAGCCGGGAGCCCGCGAGCCTAGAGCGCGTCGGTCCAGCCGCCGGGCCGCGCCGCCGCCAAGCAGCCGCCCCGCGCGCCGCGCCTCGGGAACAAAGGCGCCCGCCCGCCGCCCGCCGCCCGCGCCCGCGCCGCCGCCATGAAGCCGGGGCCGCCGCACCGTGCCGGGGCCGCCCACGGGGCCGGCGCCGGGGCCGGGGCCGCGGCCGGGCCCGGGGCCCGCGGGCTGCTCCTGCCACCGCTGCTGCTGCTGCTGCTGGCGGGGCGCGCCGCGGGGGCCCAGCGCTGGCGCAGTGAGAACTTCGAGAGACCCGTGGACCTGGAGGGCTCTGGGGATGATGACTCCTTTCCCGATGATGAACTGGATGACCTCTACTCGGGGTCGGGCTCGGGCTACTTCGAGCAGGAGTCGGGCATTGAGACAGCCATGCGCTTCAGCCCAGATGTAGCCCTGGCGGTGTCCACCACACCTGCGGTGCTGCCCACCACGAACATCCAGCCTGTGGGCACACCATTTGAAGAGCTCCCCTCTGAGCGCCCCACCCTGGAGCCAGCCACCAGCCCCCTGGTGGTGACAGAAGTCCCGGAAGAGCCCAGCCAGAGAGCCACCACCGTCTCCACTACCATGGCTACCACTGCTGCCACAAGCACAGGGGACCCGACTGTGGCCACAGTGCCTGCCACAGTGGCCACCGCCACCCCCAGCACCCCTGCAGCACCCCCTTTTACGGCCACCACTGCTGTTATAAGGACCACTGGCGTACGGAGGCTTCTGCCTCTCCCACTGACCACAGTGGCTACGGCACGGGCCACTACCCCCGAGGCGCCCTCCCCGCCCACCACGGCGGCTGTCTTGGACACCGAGGCCCCAACACCCAGGCTGGTCAGCACAGCTACCTCCCGGCCAAGAGCCCTTCCCAGGCCGGCCACCACCCAGGAGCCTGACATCCCTGAGAGGAGCACCCTGCCCCTGGGGACCACTGCCCCTGGACCCACAGAGGTGGCTCAGACCCCAACTCCAGAGACCTTCCTGACCACAATCCGGGATGAGCCAGAGGTTCCGGTGAGTGGGGGGCCCAGTGGAGACTTCGAGCTGCCAGAAGAAGAGACCACACAACCAGACACAGCCAATGAGGTGGTAGCTGTGGGAGGGGCTGCGGCCAAGGCATCATCTCCACCTGGGACACTGCCCAAGGGTGCCCGCCCGGGCCCTGGCCTCCTGGACAATGCCATCGACTCGGGCAGCTCAGCTGCTCAGCTGCCTCAGAAGAGTATCCTGGAGCGGAAGGAGGTGCTCGTAGCTGTGATTGTGGGCGGGGTGGTGGGCGCCCTCTTTGCTGCCTTCTTGGTCACACTGCTCATCTATCGTATGAAGAAAAAGGATGAGGGCAGCTACACGCTGGAGGAACCCAAGCAGGCGAGCGTCACATACCAGAAGCCTGACAAGCAGGAGGAGTTCTATGCCTAGTGGAGCCACAGTGCCTCCCTGCAGCCTCAACACCACCCTGCTGTCCAGTCCCCAGCCTGGCCCCACCAGCCCAAGC', 'proteinID': 'ENSP00000344468', 'strand': '-', 'cdnaCodingEnd': 1504, 'start': 31345982, 'biotype': 'protein_coding', 'genomicCodingStart': 31346058, 'cdnaCodingStart': 176, 'cdsLength': 1328, 'annotationFlags': ['CCDS'], 'id': 'ENST00000339394', 'chromosome': '1', 'proteinSequence': 'MKPGPPHRAGAAHGAGAGAGAAAGPGARGLLLPPLLLLLLAGRAAGAQRWRSENFERPVDLEGSGDDDSFPDDELDDLYSGSGSGYFEQESGIETAMRFSPDVALAVSTTPAVLPTTNIQPVGTPFEELPSERPTLEPATSPLVVTEVPEEPSQRATTVSTTMATTAATSTGDPTVATVPATVATATPSTPAAPPFTATTAVIRTTGVRRLLPLPLTTVATARATTPEAPSPPTTAAVLDTEAPTPRLVSTATSRPRALPRPATTQEPDIPERSTLPLGTTAPGPTEVAQTPTPETFLTTIRDEPEVPVSGGPSGDFELPEEETTQPDTANEVVAVGGAAAKASSPPGTLPKGARPGPGLLDNAIDSGSSAAQLPQKSILERKEVLVAVIVGGVVGALFAAFLVTLLIYRMKKKDEGSYTLEEPKQASVTYQKPDKQEEFYA'}, {'status': 'KNOWN', 'xrefs': [{'dbDisplayName': 'Ensembl gene', 'id': 'ENSG00000162512', 'dbName': 'ensembl_gene'}, {'dbDisplayName': 'Vega gene', 'id': 'SDC3', 'dbName': 'vega_gene'}, {'dbDisplayName': 'Ensembl transcript', 'id': 'ENST00000471567', 'dbName': 'ensembl_transcript'}, {'dbDisplayName': 'Vega transcript', 'id': 'OTTHUMT00000102018', 'dbName': 'vega_transcript'}, {'dbDisplayName': 'Vega transcript', 'id': 'SDC3-003', 'dbName': 'vega_transcript'}, {'dbDisplayName': 'HGNC transcript name', 'id': 'SDC3-003', 'dbName': 'hgnc_transcript_name'}, {'dbDisplayName': 'Havana transcript', 'id': 'OTTHUMT00000102018', 'dbName': 'havana_transcript'}], 'end': 31354276, 'name': 'SDC3-003', 'exons': [{'exonNumber': 1, 'end': 31354276, 'genomicCodingEnd': 0, 'sequence': 'CTCACCAAGGCCCACAACACGGACCCACCGCCATGGCCACGTATGTTCCCTAAACACACATCGCTCCTAGAC', 'cdsEnd': 0, 'cdnaCodingEnd': 0, 'start': 31354205, 'phase': -1, 'strand': '-', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsStart': 0, 'id': 'ENSE00001816101', 'chromosome': '1'}, {'exonNumber': 2, 'end': 31351587, 'genomicCodingEnd': 0, 'sequence': 'AGCCCGAGCCCGACCCCGAGTAGAGGTCATCCAGTTCATCATCGGGAAAGGAGTCATCATCCCCAGAGCCCTCCAGGTCCACGGGTCTCTCGAAGTTCTCACTGCGCCAGCGCTGGGC', 'cdsEnd': 0, 'cdnaCodingEnd': 0, 'start': 31351470, 'phase': -1, 'strand': '-', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsStart': 0, 'id': 'ENSE00003586093', 'chromosome': '1'}, {'exonNumber': 3, 'end': 31350012, 'genomicCodingEnd': 0, 'sequence': 'CTGTGGTCAGTGGGAGAGGCAGAAGCCTCCGTACGCCAGTGGTCCTTATAACAGCAGTGGTGGCCGTAAAAGGGGGTGCTGCAGGGGTGCTGGGGGTGGCGGTGGCCACTGTGGCAGGCACTGTGGCCACAGTCGGGTCCCCTGTGCTTGTGGCAGCAGTGGTAGCCATGGTAGTGGAGACGGTGGTGGCTCTCTGGCTGGGCTCTTCCGGGACTTCTGTCACCACCAGGGGGCTGGTGGCTGGCTCCAGGGTGGGGCGCTCAGAGGGGAGCTCTTCAAATGGTGTGCCCACAGGCTGGATGTTCGTGGTGGGCAGCACCGCAGGTGTGGTGGACACCGCCAGGGCTACATCTGGGCTGAAGCGCATGGCTGTCTCAATGCCCGACTCCTGCTCGAAGT', 'cdsEnd': 0, 'cdnaCodingEnd': 0, 'start': 31349614, 'phase': -1, 'strand': '-', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsStart': 0, 'id': 'ENSE00001662868', 'chromosome': '1'}], 'genomicCodingEnd': 0, 'cDnaSequence': 'GTCTAGGAGCGATGTGTGTTTAGGGAACATACGTGGCCATGGCGGTGGGTCCGTGTTGTGGGCCTTGGTGAGGCCCAGCGCTGGCGCAGTGAGAACTTCGAGAGACCCGTGGACCTGGAGGGCTCTGGGGATGATGACTCCTTTCCCGATGATGAACTGGATGACCTCTACTCGGGGTCGGGCTCGGGCTACTTCGAGCAGGAGTCGGGCATTGAGACAGCCATGCGCTTCAGCCCAGATGTAGCCCTGGCGGTGTCCACCACACCTGCGGTGCTGCCCACCACGAACATCCAGCCTGTGGGCACACCATTTGAAGAGCTCCCCTCTGAGCGCCCCACCCTGGAGCCAGCCACCAGCCCCCTGGTGGTGACAGAAGTCCCGGAAGAGCCCAGCCAGAGAGCCACCACCGTCTCCACTACCATGGCTACCACTGCTGCCACAAGCACAGGGGACCCGACTGTGGCCACAGTGCCTGCCACAGTGGCCACCGCCACCCCCAGCACCCCTGCAGCACCCCCTTTTACGGCCACCACTGCTGTTATAAGGACCACTGGCGTACGGAGGCTTCTGCCTCTCCCACTGACCACAG', 'strand': '-', 'cdnaCodingEnd': 0, 'start': 31349614, 'biotype': 'processed_transcript', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsLength': 0, 'id': 'ENST00000471567', 'chromosome': '1'}, {'status': 'KNOWN', 'xrefs': [{'dbDisplayName': 'Ensembl gene', 'id': 'ENSG00000162512', 'dbName': 'ensembl_gene'}, {'dbDisplayName': 'Vega gene', 'id': 'SDC3', 'dbName': 'vega_gene'}, {'dbDisplayName': 'Ensembl transcript', 'id': 'ENST00000487984', 'dbName': 'ensembl_transcript'}, {'dbDisplayName': 'Vega transcript', 'id': 'OTTHUMT00000102019', 'dbName': 'vega_transcript'}, {'dbDisplayName': 'Vega transcript', 'id': 'SDC3-004', 'dbName': 'vega_transcript'}, {'dbDisplayName': 'HGNC transcript name', 'id': 'SDC3-004', 'dbName': 'hgnc_transcript_name'}, {'dbDisplayName': 'Havana transcript', 'id': 'OTTHUMT00000102019', 'dbName': 'havana_transcript'}], 'end': 31353616, 'name': 'SDC3-004', 'exons': [{'exonNumber': 1, 'end': 31353616, 'genomicCodingEnd': 0, 'sequence': 'CTGGGATGCTCAGCGGGAACTTAATGCGAGGACACCTGGGACCTGCAGGCATGGGCGCTGGGACTCATGAGGCCCTCTCAGGAACACTACAGAGGGGGTGCTGGTAGCTGCAACTCCCAGAGGGGACAGAGAAATAGGGGTTGGGGAACGGAGCCTGGGAGGCAGCAG', 'cdsEnd': 0, 'cdnaCodingEnd': 0, 'start': 31353449, 'phase': -1, 'strand': '-', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsStart': 0, 'id': 'ENSE00001834250', 'chromosome': '1'}, {'exonNumber': 2, 'end': 31352861, 'genomicCodingEnd': 0, 'sequence': 'CTAAAAGCAGCCACAGAGGGCTCAGCGTGTCAGCATGC', 'cdsEnd': 0, 'cdnaCodingEnd': 0, 'start': 31352824, 'phase': -1, 'strand': '-', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsStart': 0, 'id': 'ENSE00001821204', 'chromosome': '1'}, {'exonNumber': 3, 'end': 31351859, 'genomicCodingEnd': 0, 'sequence': 'CTGGGGTCCCATCCCAGAAGGCTTTCAGTGTCTGGCTGATGACTTTCTCTTAGAAACTGGTCATTTTTCATCTTGACTGCACAT', 'cdsEnd': 0, 'cdnaCodingEnd': 0, 'start': 31351776, 'phase': -1, 'strand': '-', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsStart': 0, 'id': 'ENSE00001827808', 'chromosome': '1'}, {'exonNumber': 4, 'end': 31351587, 'genomicCodingEnd': 0, 'sequence': 'TCATCATCCCCAGAGCCCTCCAGGTCCACGGGTCTCTCGAAGTTCTCACTGCGCCAGCGCTGGGC', 'cdsEnd': 0, 'cdnaCodingEnd': 0, 'start': 31351523, 'phase': -1, 'strand': '-', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsStart': 0, 'id': 'ENSE00001905973', 'chromosome': '1'}], 'genomicCodingEnd': 0, 'cDnaSequence': 'CTGCTGCCTCCCAGGCTCCGTTCCCCAACCCCTATTTCTCTGTCCCCTCTGGGAGTTGCAGCTACCAGCACCCCCTCTGTAGTGTTCCTGAGAGGGCCTCATGAGTCCCAGCGCCCATGCCTGCAGGTCCCAGGTGTCCTCGCATTAAGTTCCCGCTGAGCATCCCAGGCATGCTGACACGCTGAGCCCTCTGTGGCTGCTTTTAGATGTGCAGTCAAGATGAAAAATGACCAGTTTCTAAGAGAAAGTCATCAGCCAGACACTGAAAGCCTTCTGGGATGGGACCCCAGGCCCAGCGCTGGCGCAGTGAGAACTTCGAGAGACCCGTGGACCTGGAGGGCTCTGGGGATGATGA', 'strand': '-', 'cdnaCodingEnd': 0, 'start': 31351523, 'biotype': 'processed_transcript', 'genomicCodingStart': 0, 'cdnaCodingStart': 0, 'cdsLength': 0, 'id': 'ENST00000487984', 'chromosome': '1'}], 'id': 'ENSG00000162512', 'chromosome': '1', 'description': 'syndecan 3 [Source:HGNC Symbol;Acc:HGNC:10660]'}
General genome info.
{
"properties": {
"chromosomes": {
"items": [
{
"properties": {
"cytobands": {
"items": [
{
"properties": {
"end": {
"type": "integer"
},
"name": {
"type": "string"
},
"stain": {
"type": "string"
},
"start": {
"type": "integer"
}
},
"type": "object"
}
],
"type": "array"
},
"end": {
"type": "integer"
},
"isCircular": {
"type": "integer"
},
"name": {
"type": "string"
},
"size": {
"type": "integer"
},
"start": {
"type": "integer"
}
},
"type": "object"
}
],
"type": "array"
},
"species": {
"type": "string"
},
"supercontigs": {
"items": [
{
"properties": {
"cytobands": {
"items": [
{
"properties": {
"end": {
"type": "integer"
},
"name": {
"type": "string"
},
"stain": {
"type": "string"
},
"start": {
"type": "integer"
}
},
"type": "object"
}
],
"type": "array"
},
"end": {
"type": "integer"
},
"isCircular": {
"type": "integer"
},
"name": {
"type": "string"
},
"size": {
"type": "integer"
},
"start": {
"type": "integer"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
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'end': 118800000, 'name': 'q14.1'}, {'start': 118800001, 'stain': 'gneg', 'end': 122400000, 'name': 'q14.2'}, {'start': 122400001, 'stain': 'gpos50', 'end': 129900000, 'name': 'q14.3'}, {'start': 129900001, 'stain': 'gneg', 'end': 132500000, 'name': 'q21.1'}, {'start': 132500001, 'stain': 'gpos25', 'end': 135100000, 'name': 'q21.2'}, {'start': 135100001, 'stain': 'gneg', 'end': 136800000, 'name': 'q21.3'}, {'start': 136800001, 'stain': 'gpos100', 'end': 142200000, 'name': 'q22.1'}, {'start': 142200001, 'stain': 'gneg', 'end': 144100000, 'name': 'q22.2'}, {'start': 144100001, 'stain': 'gpos100', 'end': 148700000, 'name': 'q22.3'}, {'start': 148700001, 'stain': 'gneg', 'end': 149900000, 'name': 'q23.1'}, {'start': 149900001, 'stain': 'gpos25', 'end': 150500000, 'name': 'q23.2'}, {'start': 150500001, 'stain': 'gneg', 'end': 154900000, 'name': 'q23.3'}, {'start': 154900001, 'stain': 'gpos75', 'end': 159800000, 'name': 'q24.1'}, {'start': 159800001, 'stain': 'gneg', 'end': 163700000, 'name': 'q24.2'}, {'start': 163700001, 'stain': 'gpos75', 'end': 169700000, 'name': 'q24.3'}, {'start': 169700001, 'stain': 'gneg', 'end': 178000000, 'name': 'q31.1'}, {'start': 178000001, 'stain': 'gpos50', 'end': 180600000, 'name': 'q31.2'}, {'start': 180600001, 'stain': 'gneg', 'end': 183000000, 'name': 'q31.3'}, {'start': 183000001, 'stain': 'gpos75', 'end': 189400000, 'name': 'q32.1'}, {'start': 189400001, 'stain': 'gneg', 'end': 191900000, 'name': 'q32.2'}, {'start': 191900001, 'stain': 'gpos75', 'end': 197400000, 'name': 'q32.3'}, {'start': 197400001, 'stain': 'gneg', 'end': 203300000, 'name': 'q33.1'}, {'start': 203300001, 'stain': 'gpos50', 'end': 204900000, 'name': 'q33.2'}, {'start': 204900001, 'stain': 'gneg', 'end': 209000000, 'name': 'q33.3'}, {'start': 209000001, 'stain': 'gpos100', 'end': 215300000, 'name': 'q34'}, {'start': 215300001, 'stain': 'gneg', 'end': 221500000, 'name': 'q35'}, {'start': 221500001, 'stain': 'gpos75', 'end': 225200000, 'name': 'q36.1'}, {'start': 225200001, 'stain': 'gneg', 'end': 226100000, 'name': 'q36.2'}, {'start': 226100001, 'stain': 'gpos100', 'end': 231000000, 'name': 'q36.3'}, {'start': 231000001, 'stain': 'gneg', 'end': 235600000, 'name': 'q37.1'}, {'start': 235600001, 'stain': 'gpos50', 'end': 237300000, 'name': 'q37.2'}, {'start': 237300001, 'stain': 'gneg', 'end': 243199373, 'name': 'q37.3'}], 'start': 1, 'isCircular': 0, 'size': 243199373}, {'end': 10000, 'name': 'Y', 'cytobands': [{'start': 11600001, 'stain': 'acen', 'end': 12500000, 'name': 'p11.1'}, {'start': 3000001, 'stain': 'gneg', 'end': 11600000, 'name': 'p11.2'}, {'start': 2500001, 'stain': 'gpos50', 'end': 3000000, 'name': 'p11.31'}, {'start': 1, 'stain': 'gneg', 'end': 2500000, 'name': 'p11.32'}, {'start': 12500001, 'stain': 'acen', 'end': 13400000, 'name': 'q11.1'}, {'start': 13400001, 'stain': 'gneg', 'end': 15100000, 'name': 'q11.21'}, {'start': 15100001, 'stain': 'gpos50', 'end': 19800000, 'name': 'q11.221'}, {'start': 19800001, 'stain': 'gneg', 'end': 22100000, 'name': 'q11.222'}, {'start': 22100001, 'stain': 'gpos50', 'end': 26200000, 'name': 'q11.223'}, {'start': 26200001, 'stain': 'gneg', 'end': 28800000, 'name': 'q11.23'}, {'start': 28800001, 'stain': 'gvar', 'end': 59373566, 'name': 'q12'}], 'start': 1, 'isCircular': 0, 'size': 59373566}, {'end': 59034049, 'name': 'Y', 'cytobands': [{'start': 11600001, 'stain': 'acen', 'end': 12500000, 'name': 'p11.1'}, {'start': 3000001, 'stain': 'gneg', 'end': 11600000, 'name': 'p11.2'}, {'start': 2500001, 'stain': 'gpos50', 'end': 3000000, 'name': 'p11.31'}, {'start': 1, 'stain': 'gneg', 'end': 2500000, 'name': 'p11.32'}, {'start': 12500001, 'stain': 'acen', 'end': 13400000, 'name': 'q11.1'}, {'start': 13400001, 'stain': 'gneg', 'end': 15100000, 'name': 'q11.21'}, {'start': 15100001, 'stain': 'gpos50', 'end': 19800000, 'name': 'q11.221'}, {'start': 19800001, 'stain': 'gneg', 'end': 22100000, 'name': 'q11.222'}, {'start': 22100001, 'stain': 'gpos50', 'end': 26200000, 'name': 'q11.223'}, {'start': 26200001, 'stain': 'gneg', 'end': 28800000, 'name': 'q11.23'}, {'start': 28800001, 'stain': 'gvar', 'end': 59373566, 'name': 'q12'}], 'start': 2649521, 'isCircular': 0, 'size': 59373566}, {'end': 159138663, 'name': '7', 'cytobands': [{'start': 58000001, 'stain': 'acen', 'end': 59900000, 'name': 'p11.1'}, {'start': 54000001, 'stain': 'gneg', 'end': 58000000, 'name': 'p11.2'}, {'start': 50500001, 'stain': 'gpos75', 'end': 54000000, 'name': 'p12.1'}, {'start': 49000001, 'stain': 'gneg', 'end': 50500000, 'name': 'p12.2'}, {'start': 45400001, 'stain': 'gpos75', 'end': 49000000, 'name': 'p12.3'}, {'start': 43300001, 'stain': 'gneg', 'end': 45400000, 'name': 'p13'}, {'start': 37200001, 'stain': 'gpos75', 'end': 43300000, 'name': 'p14.1'}, {'start': 35000001, 'stain': 'gneg', 'end': 37200000, 'name': 'p14.2'}, {'start': 28800001, 'stain': 'gpos75', 'end': 35000000, 'name': 'p14.3'}, {'start': 28000001, 'stain': 'gneg', 'end': 28800000, 'name': 'p15.1'}, {'start': 25500001, 'stain': 'gpos50', 'end': 28000000, 'name': 'p15.2'}, {'start': 20900001, 'stain': 'gneg', 'end': 25500000, 'name': 'p15.3'}, {'start': 16500001, 'stain': 'gpos100', 'end': 20900000, 'name': 'p21.1'}, {'start': 13800001, 'stain': 'gneg', 'end': 16500000, 'name': 'p21.2'}, {'start': 7300001, 'stain': 'gpos100', 'end': 13800000, 'name': 'p21.3'}, {'start': 4500001, 'stain': 'gneg', 'end': 7300000, 'name': 'p22.1'}, {'start': 2800001, 'stain': 'gpos25', 'end': 4500000, 'name': 'p22.2'}, {'start': 1, 'stain': 'gneg', 'end': 2800000, 'name': 'p22.3'}, {'start': 59900001, 'stain': 'acen', 'end': 61700000, 'name': 'q11.1'}, {'start': 61700001, 'stain': 'gneg', 'end': 67000000, 'name': 'q11.21'}, {'start': 67000001, 'stain': 'gpos50', 'end': 72200000, 'name': 'q11.22'}, {'start': 72200001, 'stain': 'gneg', 'end': 77500000, 'name': 'q11.23'}, {'start': 77500001, 'stain': 'gpos100', 'end': 86400000, 'name': 'q21.11'}, {'start': 86400001, 'stain': 'gneg', 'end': 88200000, 'name': 'q21.12'}, {'start': 88200001, 'stain': 'gpos75', 'end': 91100000, 'name': 'q21.13'}, {'start': 91100001, 'stain': 'gneg', 'end': 92800000, 'name': 'q21.2'}, {'start': 92800001, 'stain': 'gpos75', 'end': 98000000, 'name': 'q21.3'}, {'start': 98000001, 'stain': 'gneg', 'end': 103800000, 'name': 'q22.1'}, {'start': 103800001, 'stain': 'gpos50', 'end': 104500000, 'name': 'q22.2'}, {'start': 104500001, 'stain': 'gneg', 'end': 107400000, 'name': 'q22.3'}, {'start': 107400001, 'stain': 'gpos75', 'end': 114600000, 'name': 'q31.1'}, {'start': 114600001, 'stain': 'gneg', 'end': 117400000, 'name': 'q31.2'}, {'start': 117400001, 'stain': 'gpos75', 'end': 121100000, 'name': 'q31.31'}, {'start': 121100001, 'stain': 'gneg', 'end': 123800000, 'name': 'q31.32'}, {'start': 123800001, 'stain': 'gpos75', 'end': 127100000, 'name': 'q31.33'}, {'start': 127100001, 'stain': 'gneg', 'end': 129200000, 'name': 'q32.1'}, {'start': 129200001, 'stain': 'gpos25', 'end': 130400000, 'name': 'q32.2'}, {'start': 130400001, 'stain': 'gneg', 'end': 132600000, 'name': 'q32.3'}, {'start': 132600001, 'stain': 'gpos50', 'end': 138200000, 'name': 'q33'}, {'start': 138200001, 'stain': 'gneg', 'end': 143100000, 'name': 'q34'}, {'start': 143100001, 'stain': 'gpos75', 'end': 147900000, 'name': 'q35'}, {'start': 147900001, 'stain': 'gneg', 'end': 152600000, 'name': 'q36.1'}, {'start': 152600001, 'stain': 'gpos25', 'end': 155100000, 'name': 'q36.2'}, {'start': 155100001, 'stain': 'gneg', 'end': 159138663, 'name': 'q36.3'}], 'start': 1, 'isCircular': 0, 'size': 159138663}, {'end': 48129895, 'name': '21', 'cytobands': [{'start': 10900001, 'stain': 'acen', 'end': 13200000, 'name': 'p11.1'}, {'start': 6800001, 'stain': 'gvar', 'end': 10900000, 'name': 'p11.2'}, {'start': 2800001, 'stain': 'stalk', 'end': 6800000, 'name': 'p12'}, {'start': 1, 'stain': 'gvar', 'end': 2800000, 'name': 'p13'}, {'start': 13200001, 'stain': 'acen', 'end': 14300000, 'name': 'q11.1'}, {'start': 14300001, 'stain': 'gneg', 'end': 16400000, 'name': 'q11.2'}, {'start': 16400001, 'stain': 'gpos100', 'end': 24000000, 'name': 'q21.1'}, {'start': 24000001, 'stain': 'gneg', 'end': 26800000, 'name': 'q21.2'}, {'start': 26800001, 'stain': 'gpos75', 'end': 31500000, 'name': 'q21.3'}, {'start': 31500001, 'stain': 'gneg', 'end': 35800000, 'name': 'q22.11'}, {'start': 35800001, 'stain': 'gpos50', 'end': 37800000, 'name': 'q22.12'}, {'start': 37800001, 'stain': 'gneg', 'end': 39700000, 'name': 'q22.13'}, {'start': 39700001, 'stain': 'gpos50', 'end': 42600000, 'name': 'q22.2'}, {'start': 42600001, 'stain': 'gneg', 'end': 48129895, 'name': 'q22.3'}], 'start': 1, 'isCircular': 0, 'size': 48129895}, {'end': 135006516, 'name': '11', 'cytobands': [{'start': 51600001, 'stain': 'acen', 'end': 53700000, 'name': 'p11.11'}, {'start': 48800001, 'stain': 'gpos75', 'end': 51600000, 'name': 'p11.12'}, {'start': 43500001, 'stain': 'gneg', 'end': 48800000, 'name': 'p11.2'}, {'start': 36400001, 'stain': 'gpos100', 'end': 43500000, 'name': 'p12'}, {'start': 31000001, 'stain': 'gneg', 'end': 36400000, 'name': 'p13'}, {'start': 27200001, 'stain': 'gpos75', 'end': 31000000, 'name': 'p14.1'}, {'start': 26100001, 'stain': 'gneg', 'end': 27200000, 'name': 'p14.2'}, {'start': 21700001, 'stain': 'gpos100', 'end': 26100000, 'name': 'p14.3'}, {'start': 16200001, 'stain': 'gneg', 'end': 21700000, 'name': 'p15.1'}, {'start': 12700001, 'stain': 'gpos50', 'end': 16200000, 'name': 'p15.2'}, {'start': 10700001, 'stain': 'gneg', 'end': 12700000, 'name': 'p15.3'}, {'start': 2800001, 'stain': 'gpos50', 'end': 10700000, 'name': 'p15.4'}, {'start': 1, 'stain': 'gneg', 'end': 2800000, 'name': 'p15.5'}, {'start': 53700001, 'stain': 'acen', 'end': 55700000, 'name': 'q11'}, {'start': 55700001, 'stain': 'gpos75', 'end': 59900000, 'name': 'q12.1'}, {'start': 59900001, 'stain': 'gneg', 'end': 61700000, 'name': 'q12.2'}, {'start': 61700001, 'stain': 'gpos25', 'end': 63400000, 'name': 'q12.3'}, {'start': 63400001, 'stain': 'gneg', 'end': 65900000, 'name': 'q13.1'}, {'start': 65900001, 'stain': 'gpos25', 'end': 68400000, 'name': 'q13.2'}, {'start': 68400001, 'stain': 'gneg', 'end': 70400000, 'name': 'q13.3'}, {'start': 70400001, 'stain': 'gpos50', 'end': 75200000, 'name': 'q13.4'}, {'start': 75200001, 'stain': 'gneg', 'end': 77100000, 'name': 'q13.5'}, {'start': 77100001, 'stain': 'gpos100', 'end': 85600000, 'name': 'q14.1'}, {'start': 85600001, 'stain': 'gneg', 'end': 88300000, 'name': 'q14.2'}, {'start': 88300001, 'stain': 'gpos100', 'end': 92800000, 'name': 'q14.3'}, {'start': 92800001, 'stain': 'gneg', 'end': 97200000, 'name': 'q21'}, {'start': 97200001, 'stain': 'gpos100', 'end': 102100000, 'name': 'q22.1'}, {'start': 102100001, 'stain': 'gneg', 'end': 102900000, 'name': 'q22.2'}, {'start': 102900001, 'stain': 'gpos100', 'end': 110400000, 'name': 'q22.3'}, {'start': 110400001, 'stain': 'gneg', 'end': 112500000, 'name': 'q23.1'}, {'start': 112500001, 'stain': 'gpos50', 'end': 114500000, 'name': 'q23.2'}, {'start': 114500001, 'stain': 'gneg', 'end': 121200000, 'name': 'q23.3'}, {'start': 121200001, 'stain': 'gpos50', 'end': 123900000, 'name': 'q24.1'}, {'start': 123900001, 'stain': 'gneg', 'end': 127800000, 'name': 'q24.2'}, {'start': 127800001, 'stain': 'gpos50', 'end': 130800000, 'name': 'q24.3'}, {'start': 130800001, 'stain': 'gneg', 'end': 135006516, 'name': 'q25'}], 'start': 1, 'isCircular': 0, 'size': 135006516}, {'end': 16569, 'name': 'MT', 'cytobands': [{'start': 1, 'stain': 'gneg', 'end': 16569, 'name': ''}], 'start': 1, 'isCircular': 0, 'size': 16569}], 'species': 'Homo sapiens'}
Chromosome sequences.
{
"properties": {
"_chunkIds": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"assembly": {
"type": "string"
},
"chunkId": {
"type": "string"
},
"end": {
"type": "integer"
},
"sequence": {
"type": "string"
},
"sequenceName": {
"type": "string"
},
"sequenceType": {
"type": "string"
},
"start": {
"type": "integer"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'end': 1999, 'sequence': 'NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN', '_chunkIds': ['1_0_2k'], 'chunkId': '1_0_2k', 'start': 1, 'sequenceName': '1', 'assembly': 'GRCh37', 'sequenceType': 'chromosome'}
Conservation scores per genomic position, e.g. PhastCons, PhyloP.
{
"properties": {
"_chunkIds": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"chromosome": {
"type": "string"
},
"chunkId": {
"type": "integer"
},
"end": {
"type": "integer"
},
"start": {
"type": "integer"
},
"type": {
"type": "string"
},
"values": {
"items": [
{
"type": "number"
}
],
"type": "array"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'end': 2269999, '_chunkIds': ['8_1134_2k'], 'chunkId': 1134, 'start': 2269849, 'values': [0.006, 0.013, 0.018, 0.024, 0.028, 0.031, 0.033, 0.034, 0.035, 0.034, 0.032, 0.036, 0.038, 0.04, 0.041, 0.049, 0.055, 0.058, 0.06, 0.06, 0.057, 0.052, 0.054, 0.054, 0.052, 0.038, 0.03, 0.02, 0.006, 0.001, 0.001, 0.001, 0.0, 0.001, 0.001, 0.003, 0.004, 0.007, 0.008, 0.009, 0.009, 0.007, 0.007, 0.007, 0.008, 0.014, 0.017, 0.027, 0.035, 0.04, 0.043, 0.045, 0.045, 0.043, 0.04, 0.045, 0.048, 0.052, 0.054, 0.056, 0.058, 0.059, 0.059, 0.059, 0.055, 0.053, 0.051, 0.048, 0.044, 0.04, 0.035, 0.03, 0.031, 0.031, 0.031, 0.031, 0.03, 0.028, 0.026, 0.023, 0.026, 0.028, 0.03, 0.03, 0.03, 0.03, 0.029, 0.027, 0.024, 0.02, 0.016, 0.016, 0.016, 0.015, 0.014, 0.012, 0.009, 0.006, 0.006, 0.005, 0.003, 0.004, 0.004, 0.005, 0.006, 0.007, 0.007, 0.006, 0.005, 0.007, 0.007, 0.007, 0.007, 0.009, 0.01, 0.011, 0.011, 0.016, 0.02, 0.023, 0.025, 0.027, 0.028, 0.028, 0.028, 0.027, 0.025, 0.022, 0.019, 0.015, 0.011, 0.006, 0.004, 0.005, 0.005, 0.004, 0.006, 0.006, 0.007, 0.007, 0.009, 0.018, 0.026, 0.033, 0.039, 0.045, 0.05, 0.053, 0.057, 0.059], 'type': 'phastCons', 'chromosome': '8'}
Protein annotation from UniProt and InterPro.
{
"properties": {
"accession": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"comment": {
"items": [
{
"properties": {
"event": {
"items": [],
"type": "array"
},
"evidence": {
"items": [],
"type": "array"
},
"interactant": {
"items": [],
"type": "array"
},
"isoform": {
"items": [],
"type": "array"
},
"link": {
"items": [],
"type": "array"
},
"location": {
"items": [],
"type": "array"
},
"subcellularLocation": {
"items": [],
"type": "array"
},
"text": {
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"value": {
"type": "string"
}
},
"type": "object"
},
"type": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"created": {
"type": "integer"
},
"dataset": {
"type": "string"
},
"dbReference": {
"items": [
{
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"id": {
"type": "string"
},
"property": {
"items": [
{
"properties": {
"type": {
"type": "string"
},
"value": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"type": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"evidence": {
"items": [],
"type": "array"
},
"feature": {
"items": [
{
"properties": {
"description": {
"type": "string"
},
"evidence": {
"items": [],
"type": "array"
},
"id": {
"type": "string"
},
"location": {
"properties": {
"begin": {
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"position": {
"type": "integer"
},
"status": {
"type": "string"
}
},
"type": "object"
},
"end": {
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"position": {
"type": "integer"
},
"status": {
"type": "string"
}
},
"type": "object"
}
},
"type": "object"
},
"type": {
"type": "string"
},
"variation": {
"items": [],
"type": "array"
}
},
"type": "object"
}
],
"type": "array"
},
"gene": {
"items": [
{
"properties": {
"name": {
"items": [
{
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"type": {
"type": "string"
},
"value": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
}
],
"type": "array"
},
"geneLocation": {
"items": [],
"type": "array"
},
"keyword": {
"items": [
{
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"id": {
"type": "string"
},
"value": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"modified": {
"type": "integer"
},
"name": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"organism": {
"properties": {
"dbReference": {
"items": [
{
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"id": {
"type": "string"
},
"property": {
"items": [],
"type": "array"
},
"type": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"evidence": {
"items": [],
"type": "array"
},
"lineage": {
"properties": {
"taxon": {
"items": [
{
"type": "string"
}
],
"type": "array"
}
},
"type": "object"
},
"name": {
"items": [
{
"properties": {
"type": {
"type": "string"
},
"value": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
},
"organismHost": {
"items": [],
"type": "array"
},
"protein": {
"properties": {
"alternativeName": {
"items": [
{
"properties": {
"ecNumber": {
"items": [],
"type": "array"
},
"fullName": {
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"value": {
"type": "string"
}
},
"type": "object"
},
"shortName": {
"items": [],
"type": "array"
}
},
"type": "object"
}
],
"type": "array"
},
"cdAntigenName": {
"items": [],
"type": "array"
},
"component": {
"items": [],
"type": "array"
},
"domain": {
"items": [],
"type": "array"
},
"innName": {
"items": [],
"type": "array"
},
"recommendedName": {
"properties": {
"ecNumber": {
"items": [],
"type": "array"
},
"fullName": {
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"value": {
"type": "string"
}
},
"type": "object"
},
"shortName": {
"items": [],
"type": "array"
}
},
"type": "object"
},
"submittedName": {
"items": [],
"type": "array"
}
},
"type": "object"
},
"proteinExistence": {
"properties": {
"type": {
"type": "string"
}
},
"type": "object"
},
"reference": {
"items": [
{
"properties": {
"citation": {
"properties": {
"authorList": {
"properties": {
"consortiumOrPerson": {
"items": [
{
"properties": {
"name": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
},
"date": {
"type": "string"
},
"dbReference": {
"items": [
{
"properties": {
"evidence": {
"items": [],
"type": "array"
},
"id": {
"type": "string"
},
"property": {
"items": [],
"type": "array"
},
"type": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"first": {
"type": "string"
},
"last": {
"type": "string"
},
"name": {
"type": "string"
},
"title": {
"type": "string"
},
"type": {
"type": "string"
},
"volume": {
"type": "string"
}
},
"type": "object"
},
"evidence": {
"items": [],
"type": "array"
},
"key": {
"type": "string"
},
"scope": {
"items": [
{
"type": "string"
}
],
"type": "array"
}
},
"type": "object"
}
],
"type": "array"
},
"sequence": {
"properties": {
"checksum": {
"type": "string"
},
"length": {
"type": "integer"
},
"mass": {
"type": "integer"
},
"modified": {
"type": "integer"
},
"value": {
"type": "string"
},
"version": {
"type": "integer"
}
},
"type": "object"
},
"version": {
"type": "integer"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'comment': [{'text': {'value': 'Product of a dubious gene prediction. Overlap the RAB4A locus.', 'evidence': []}, 'isoform': [], 'interactant': [], 'evidence': [], 'subcellularLocation': [], 'link': [], 'location': [], 'type': 'caution', 'event': []}], 'evidence': [], 'name': ['HRES1_HUMAN'], 'organismHost': [], 'sequence': {'checksum': '2D5FF7717B0E22E2', 'modified': 846806400000L, 'value': 'MRCAHAPAPRTRYPTRAPSGPRPPSRSQAQTPPRSVPRLRPRHRHPQDPRSPGPAPRHRRPPRPDPRAPPARASYRRFRTWPSATSWERRRLSPGHRALARGPPARLGGEGPGAGDRRREGPDRSPRQPPVLPAAAAQPDSSSAQAPGPSTLRPAATARRKRRWATRGPAHPAFARAHGEAGAGRVRTSARAGSTCAGWALWRCALRWAERQVGALGAESRFP', 'length': 223, 'version': 1, 'mass': 24343}, 'created': 1202169600000L, 'geneLocation': [], 'accession': ['P13985'], 'dbReference': [{'property': [{'type': 'protein sequence ID', 'value': 'CAA34646.1'}, {'type': 'molecule type', 'value': 'Genomic_DNA'}], 'type': 'EMBL', 'id': 'X16660', 'evidence': []}, {'property': [{'type': 'entry name', 'value': 'S06705'}], 'type': 'PIR', 'id': 'S06705', 'evidence': []}, {'property': [], 'type': 'PhosphoSite', 'id': 'P13985', 'evidence': []}, {'property': [], 'type': 'DMDM', 'id': '74739729', 'evidence': []}, {'property': [], 'type': 'PRIDE', 'id': 'P13985', 'evidence': []}, {'property': [], 'type': 'GeneCards', 'id': 'GC01U990083', 'evidence': []}, {'property': [{'type': 'gene designation', 'value': 'HRES1'}], 'type': 'HGNC', 'id': 'HGNC:5180', 'evidence': []}, {'property': [{'type': 'type', 'value': 'gene'}], 'type': 'MIM', 'id': '143025', 'evidence': []}, {'property': [], 'type': 'neXtProt', 'id': 'NX_P13985', 'evidence': []}, {'property': [], 'type': 'Genevestigator', 'id': 'P13985', 'evidence': []}], 'feature': [{'description': 'Putative HTLV-1-related endogenous sequence', 'variation': [], 'evidence': [], 'location': {'begin': {'status': 'certain', 'position': 1, 'evidence': []}, 'end': {'status': 'certain', 'position': 223, 'evidence': []}}, 'type': 'chain', 'id': 'PRO_0000317386'}], 'version': 47, 'keyword': [{'id': 'KW-0181', 'value': 'Complete proteome', 'evidence': []}, {'id': 'KW-1185', 'value': 'Reference proteome', 'evidence': []}], 'modified': 1390348800000L, 'dataset': 'Swiss-Prot', 'protein': {'domain': [], 'alternativeName': [{'fullName': {'value': 'p25', 'evidence': []}, 'shortName': [], 'ecNumber': []}], 'component': [], 'innName': [], 'cdAntigenName': [], 'recommendedName': {'fullName': {'value': 'Putative HTLV-1-related endogenous sequence', 'evidence': []}, 'shortName': [], 'ecNumber': []}, 'submittedName': []}, 'gene': [{'name': [{'type': 'primary', 'value': 'HRES1', 'evidence': []}]}], 'organism': {'lineage': {'taxon': ['Eukaryota', 'Metazoa', 'Chordata', 'Craniata', 'Vertebrata', 'Euteleostomi', 'Mammalia', 'Eutheria', 'Euarchontoglires', 'Primates', 'Haplorrhini', 'Catarrhini', 'Hominidae', 'Homo']}, 'name': [{'type': 'scientific', 'value': 'Homo sapiens'}, {'type': 'common', 'value': 'Human'}], 'dbReference': [{'property': [], 'type': 'NCBI Taxonomy', 'id': '9606', 'evidence': []}], 'evidence': []}, 'reference': [{'scope': ['NUCLEOTIDE SEQUENCE [GENOMIC DNA]'], 'citation': {'authorList': {'consortiumOrPerson': [{'name': 'Perl A.'}, {'name': 'Rosenblatt J.D.'}, {'name': 'Chen I.S.'}, {'name': 'DiVincenzo J.P.'}, {'name': 'Bever R.'}, {'name': 'Poiesz B.J.'}, {'name': 'Abraham G.N.'}]}, 'last': '6854', 'name': 'Nucleic Acids Res.', 'title': 'Detection and cloning of new HTLV-related endogenous sequences in man.', 'dbReference': [{'property': [], 'type': 'DOI', 'id': '10.1093/nar/17.17.6841', 'evidence': []}, {'property': [], 'type': 'PubMed', 'id': '2780312', 'evidence': []}], 'volume': '17', 'date': '1989', 'type': 'journal article', 'first': '6841'}, 'key': '1', 'evidence': []}], 'proteinExistence': {'type': 'uncertain'}}
Variant effect prediction scores such as SIFT or Polyphen for each aminoacid change.
{
"properties": {
"aaPositions": {
"properties": {
"1": {
"properties": {
"A": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"C": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"D": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"E": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"F": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"G": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"H": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"I": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"K": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"L": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"M": {
"properties": {
"pe": {
"type": "null"
},
"ps": {
"type": "null"
}
},
"type": "object"
},
"N": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"P": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Q": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"R": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"S": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"T": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"V": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"W": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Y": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
}
},
"type": "object"
},
"2": {
"properties": {
"A": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"C": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"D": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"E": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"F": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"G": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"H": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"I": {
"properties": {
"pe": {
"type": "null"
},
"ps": {
"type": "null"
}
},
"type": "object"
},
"K": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"L": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"M": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"N": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"P": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Q": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"R": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"S": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"T": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"V": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"W": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Y": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
}
},
"type": "object"
},
"3": {
"properties": {
"A": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"C": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"D": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"E": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"F": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"G": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"H": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"I": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"K": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"L": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"M": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"N": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"P": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Q": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"R": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"S": {
"properties": {
"pe": {
"type": "null"
},
"ps": {
"type": "null"
}
},
"type": "object"
},
"T": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"V": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"W": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Y": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
}
},
"type": "object"
},
"4": {
"properties": {
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"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"C": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"D": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"E": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"F": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"G": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"H": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"I": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"K": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"L": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"M": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"N": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"P": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Q": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"R": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"S": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"T": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"V": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"W": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Y": {
"properties": {
"pe": {
"type": "null"
},
"ps": {
"type": "null"
}
},
"type": "object"
}
},
"type": "object"
},
"5": {
"properties": {
"A": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"C": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"D": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"E": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"F": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"G": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"H": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"I": {
"properties": {
"pe": {
"type": "null"
},
"ps": {
"type": "null"
}
},
"type": "object"
},
"K": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"L": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"M": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"N": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"P": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Q": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"R": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"S": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"T": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"V": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"W": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
},
"Y": {
"properties": {
"pe": {
"type": "integer"
},
"ps": {
"type": "number"
}
},
"type": "object"
}
},
"type": "object"
}
},
"type": "object"
},
"checksum": {
"type": "string"
},
"size": {
"type": "integer"
},
"transcriptId": {
"type": "string"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'size': 5, 'checksum': 'bbac0f119ec291d3260463db5c0aa0d9', 'aaPositions': {'1': {'A': {'ps': 0.644, 'pe': 1}, 'C': {'ps': 0.963, 'pe': 0}, 'E': {'ps': 0.669, 'pe': 1}, 'D': {'ps': 0.898, 'pe': 1}, 'G': {'ps': 0.792, 'pe': 1}, 'F': {'ps': 0.887, 'pe': 1}, 'I': {'ps': 0.78, 'pe': 1}, 'H': {'ps': 0.951, 'pe': 0}, 'K': {'ps': 0.472, 'pe': 1}, 'M': {'ps': None, 'pe': None}, 'L': {'ps': 0.415, 'pe': 2}, 'N': {'ps': 0.794, 'pe': 1}, 'Q': {'ps': 0.734, 'pe': 1}, 'P': {'ps': 0.928, 'pe': 0}, 'S': {'ps': 0.644, 'pe': 1}, 'R': {'ps': 0.039, 'pe': 2}, 'T': {'ps': 0.706, 'pe': 1}, 'W': {'ps': 0.983, 'pe': 0}, 'V': {'ps': 0.706, 'pe': 1}, 'Y': {'ps': 0.928, 'pe': 0}}, '3': {'A': {'ps': 0.659, 'pe': 1}, 'C': {'ps': 0.975, 'pe': 0}, 'E': {'ps': 0.808, 'pe': 1}, 'D': {'ps': 0.853, 'pe': 1}, 'G': {'ps': 0.792, 'pe': 1}, 'F': {'ps': 0.827, 'pe': 1}, 'I': {'ps': 0.906, 'pe': 1}, 'H': {'ps': 0.936, 'pe': 0}, 'K': {'ps': 0.808, 'pe': 1}, 'M': {'ps': 0.976, 'pe': 0}, 'L': {'ps': 0.685, 'pe': 1}, 'N': {'ps': 0.923, 'pe': 0}, 'Q': {'ps': 0.952, 'pe': 0}, 'P': {'ps': 0.058, 'pe': 2}, 'S': {'ps': None, 'pe': None}, 'R': {'ps': 0.93, 'pe': 0}, 'T': {'ps': 0.785, 'pe': 1}, 'W': {'ps': 0.976, 'pe': 0}, 'V': {'ps': 0.808, 'pe': 1}, 'Y': {'ps': 0.096, 'pe': 2}}, '2': {'A': {'ps': 0.994, 'pe': 0}, 'C': {'ps': 0.999, 'pe': 0}, 'E': {'ps': 0.999, 'pe': 0}, 'D': {'ps': 0.999, 'pe': 0}, 'G': {'ps': 0.998, 'pe': 0}, 'F': {'ps': 0.998, 'pe': 0}, 'I': {'ps': None, 'pe': None}, 'H': {'ps': 0.999, 'pe': 0}, 'K': {'ps': 0.999, 'pe': 0}, 'M': {'ps': 0.999, 'pe': 0}, 'L': {'ps': 0.986, 'pe': 0}, 'N': {'ps': 0.999, 'pe': 0}, 'Q': {'ps': 0.999, 'pe': 0}, 'P': {'ps': 0.999, 'pe': 0}, 'S': {'ps': 0.998, 'pe': 0}, 'R': {'ps': 0.999, 'pe': 0}, 'T': {'ps': 0.997, 'pe': 0}, 'W': {'ps': 0.999, 'pe': 0}, 'V': {'ps': 0.986, 'pe': 0}, 'Y': {'ps': 0.999, 'pe': 0}}, '5': {'A': {'ps': 0.792, 'pe': 1}, 'C': {'ps': 0.982, 'pe': 0}, 'E': {'ps': 0.976, 'pe': 0}, 'D': {'ps': 0.976, 'pe': 0}, 'G': {'ps': 0.965, 'pe': 0}, 'F': {'ps': 0.904, 'pe': 1}, 'I': {'ps': None, 'pe': None}, 'H': {'ps': 0.982, 'pe': 0}, 'K': {'ps': 0.949, 'pe': 0}, 'M': {'ps': 0.951, 'pe': 0}, 'L': {'ps': 0.078, 'pe': 2}, 'N': {'ps': 0.975, 'pe': 0}, 'Q': {'ps': 0.976, 'pe': 0}, 'P': {'ps': 0.976, 'pe': 0}, 'S': {'ps': 0.963, 'pe': 0}, 'R': {'ps': 0.976, 'pe': 0}, 'T': {'ps': 0.915, 'pe': 0}, 'W': {'ps': 0.982, 'pe': 0}, 'V': {'ps': 0.437, 'pe': 2}, 'Y': {'ps': 0.976, 'pe': 0}}, '4': {'A': {'ps': 0.955, 'pe': 0}, 'C': {'ps': 0.99, 'pe': 0}, 'E': {'ps': 0.981, 'pe': 0}, 'D': {'ps': 0.987, 'pe': 0}, 'G': {'ps': 0.972, 'pe': 0}, 'F': {'ps': 0.78, 'pe': 1}, 'I': {'ps': 0.972, 'pe': 0}, 'H': {'ps': 0.987, 'pe': 0}, 'K': {'ps': 0.981, 'pe': 0}, 'M': {'ps': 0.99, 'pe': 0}, 'L': {'ps': 0.889, 'pe': 1}, 'N': {'ps': 0.987, 'pe': 0}, 'Q': {'ps': 0.987, 'pe': 0}, 'P': {'ps': 0.987, 'pe': 0}, 'S': {'ps': 0.98, 'pe': 0}, 'R': {'ps': 0.987, 'pe': 0}, 'T': {'ps': 0.981, 'pe': 0}, 'W': {'ps': 0.219, 'pe': 2}, 'V': {'ps': 0.955, 'pe': 0}, 'Y': {'ps': None, 'pe': None}}}, 'transcriptId': 'ENST00000430747'}
PPI data from Intact.
{
"properties": {
"authors": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"detectionMethod": {
"items": [
{
"properties": {
"name": {
"type": "string"
},
"psimi": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"interactorA": {
"properties": {
"biologicalRole": {
"items": [
{
"properties": {
"name": {
"type": "string"
},
"psimi": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"dbName": {
"type": "string"
},
"id": {
"type": "string"
},
"moleculeType": {
"properties": {
"name": {
"type": "string"
},
"psimi": {
"type": "string"
}
},
"type": "object"
},
"xrefs": {
"items": [
{
"properties": {
"dbName": {
"type": "string"
},
"description": {
"type": "string"
},
"id": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
},
"interactorB": {
"properties": {
"biologicalRole": {
"items": [
{
"properties": {
"name": {
"type": "string"
},
"psimi": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"dbName": {
"type": "string"
},
"id": {
"type": "string"
},
"moleculeType": {
"properties": {
"name": {
"type": "string"
},
"psimi": {
"type": "string"
}
},
"type": "object"
},
"xrefs": {
"items": [
{
"properties": {
"dbName": {
"type": "string"
},
"description": {
"type": "string"
},
"id": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
},
"pubmed": {
"type": "string"
},
"score": {
"items": [
{
"properties": {
"score": {
"type": "number"
},
"type": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"source": {
"items": [
{
"properties": {
"name": {
"type": "string"
},
"psimi": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"status": {
"type": "string"
},
"type": {
"items": [
{
"properties": {
"name": {
"type": "string"
},
"psimi": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
},
"xrefs": {
"items": [
{
"properties": {
"dbName": {
"type": "string"
},
"id": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'status': 'curated', 'xrefs': [{'id': 'MINT-5214823', 'dbName': 'mint'}, {'id': 'EBI-495141', 'dbName': 'intact'}], 'detectionMethod': [{'psimi': 'MI:0030', 'name': 'cross-linking study'}], 'pubmed': '11717445', 'interactorA': {'moleculeType': {'psimi': 'MI:0326', 'name': 'protein'}, 'biologicalRole': [{'psimi': 'MI:0499', 'name': 'unspecified role'}], 'xrefs': [{'id': 'Q92851-3', 'dbName': 'uniprotkb'}, {'id': 'EBI-495122', 'dbName': 'intact'}, {'id': 'q92851-3', 'dbName': 'display_long'}, {'id': '10-C', 'dbName': 'isoform synonym'}, {'id': 'CASP10', 'dbName': 'gene name'}, {'id': 'CASP10', 'dbName': 'display_short'}, {'id': 'MCH4', 'dbName': 'gene name synonym'}, {'id': 'Apoptotic protease Mch-4', 'dbName': 'gene name synonym'}, {'id': 'FAS-associated death domain protein interleukin-1B-converting enzyme 2', 'dbName': 'gene name synonym'}, {'id': 'ICE-like apoptotic protease 4', 'dbName': 'gene name synonym'}, {'description': 'caspa_human', 'id': 'EBI-495095', 'dbName': 'intact'}], 'id': 'Q92851-3', 'dbName': 'uniprotkb'}, 'interactorB': {'moleculeType': {'psimi': 'MI:0326', 'name': 'protein'}, 'biologicalRole': [{'psimi': 'MI:0499', 'name': 'unspecified role'}], 'xrefs': [{'id': 'Q92851-3', 'dbName': 'uniprotkb'}, {'id': 'EBI-495122', 'dbName': 'intact'}, {'id': 'q92851-3', 'dbName': 'display_long'}, {'id': '10-C', 'dbName': 'isoform synonym'}, {'id': 'CASP10', 'dbName': 'gene name'}, {'id': 'CASP10', 'dbName': 'display_short'}, {'id': 'MCH4', 'dbName': 'gene name synonym'}, {'id': 'Apoptotic protease Mch-4', 'dbName': 'gene name synonym'}, {'id': 'FAS-associated death domain protein interleukin-1B-converting enzyme 2', 'dbName': 'gene name synonym'}, {'id': 'ICE-like apoptotic protease 4', 'dbName': 'gene name synonym'}, {'description': 'caspa_human', 'id': 'EBI-495095', 'dbName': 'intact'}], 'id': 'Q92851-3', 'dbName': 'uniprotkb'}, 'score': [{'score': 0.4, 'type': 'intact-miscore'}], 'source': [{'psimi': 'MI:0471', 'name': 'MINT'}], 'authors': ['Wang et al. (2001)'], 'type': [{'psimi': 'MI:0915', 'name': 'physical association'}]}
Regulatory annotation.
{
"properties": {
"_chunkIds": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"alias": {
"type": "string"
},
"cellTypes": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"chromosome": {
"type": "string"
},
"chunkIds": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"end": {
"type": "integer"
},
"featureClass": {
"type": "string"
},
"featureType": {
"type": "string"
},
"frame": {
"type": "string"
},
"name": {
"type": "string"
},
"score": {
"type": "string"
},
"source": {
"type": "string"
},
"start": {
"type": "integer"
},
"strand": {
"type": "string"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'alias': 'HUVEC_CTCF_ENCODE_Uw_SWEMBL_R015', 'featureType': 'TF_binding_site', 'chunkIds': ['19_133_2k'], 'end': 267744, 'name': 'CTCF', 'start': 267159, 'frame': '.', '_chunkIds': ['19_133_2k'], 'cellTypes': ['HUVEC'], 'source': 'SWEmbl_R015', 'score': '.', 'strand': '.', 'featureClass': 'Transcription Factor', 'chromosome': '19'}
Genomic variant data from ENSEMBL variation. Includes CellBase variant annotation and population frequenciesfrom ExAC, 1K genomes phase 1 and 3, GoNL, UK10K, etc.
{
"properties": {
"alleleString": {
"type": "string"
},
"alternate": {
"type": "string"
},
"ancestralAllele": {
"type": "string"
},
"chromosome": {
"type": "string"
},
"chunkIds": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"consequenceTypes": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"displayConsequenceType": {
"type": "string"
},
"end": {
"type": "integer"
},
"evidence": {
"type": "string"
},
"id": {
"type": "string"
},
"minorAllele": {
"type": "string"
},
"minorAlleleFreq": {
"type": "string"
},
"phenotype": {
"type": "null"
},
"populationFrequencies": {
"items": [],
"type": "array"
},
"reference": {
"type": "string"
},
"samples": {
"type": "null"
},
"start": {
"type": "integer"
},
"strand": {
"type": "string"
},
"transcriptVariations": {
"items": [
{
"properties": {
"alleleString": {
"type": "string"
},
"cdnaEnd": {
"type": "integer"
},
"cdnaStart": {
"type": "integer"
},
"cdsEnd": {
"type": "integer"
},
"cdsStart": {
"type": "integer"
},
"codonAlleleString": {
"type": "string"
},
"consequenceTypes": {
"items": [
{
"type": "string"
}
],
"type": "array"
},
"distanceToTranscript": {
"type": "integer"
},
"hgvsGenomic": {
"type": "string"
},
"hgvsProtein": {
"type": "string"
},
"hgvsTranscript": {
"type": "string"
},
"peptideAlleleString": {
"type": "string"
},
"polyphenPrediction": {
"type": "string"
},
"polyphenScore": {
"type": "number"
},
"siftPrediction": {
"type": "string"
},
"siftScore": {
"type": "number"
},
"somatic": {
"type": "string"
},
"transcriptId": {
"type": "string"
},
"translationEnd": {
"type": "integer"
},
"translationStart": {
"type": "integer"
}
},
"type": "object"
}
],
"type": "array"
},
"type": {
"type": "string"
},
"validationStatus": {
"type": "string"
},
"xrefs": {
"items": [
{
"properties": {
"crossReference": {
"type": "string"
},
"dataBase": {
"type": "string"
},
"version": {
"type": "string"
}
},
"type": "object"
}
],
"type": "array"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'reference': 'A', 'validationStatus': '', 'evidence': 'Multiple_observations', 'populationFrequencies': [], 'displayConsequenceType': 'intron_variant', 'id': 'rs600183', 'chromosome': 'HSCHR19LRC_PGF2_CTG1', 'end': 54989681, 'alternate': 'G', 'minorAllele': '', 'start': 54989681, 'consequenceTypes': ['intron_variant'], 'phenotype': None, 'samples': None, 'type': 'SNV', 'xrefs': [{'crossReference': 'rs2364439', 'version': '138', 'dataBase': 'Archive dbSNP'}], 'ancestralAllele': '', 'alleleString': 'A/G', 'strand': '1', 'chunkIds': ['HSCHR19LRC_PGF2_CTG1_10997_5k'], 'transcriptVariations': [{'siftScore': 0.0, 'cdnaStart': 0, 'codonAlleleString': '', 'transcriptId': 'ENST00000576413', 'translationStart': 0, 'hgvsProtein': '', 'cdsEnd': 0, 'cdnaEnd': 0, 'somatic': '0', 'distanceToTranscript': 10278, 'consequenceTypes': ['intron_variant'], 'peptideAlleleString': '', 'translationEnd': 0, 'cdsStart': 0, 'polyphenPrediction': '', 'hgvsTranscript': 'ENST00000576413.1:c.35-4618G>A', 'hgvsGenomic': '', 'alleleString': 'G/A', 'polyphenScore': 0.0, 'siftPrediction': ''}, {'siftScore': 0.0, 'cdnaStart': 0, 'codonAlleleString': '', 'transcriptId': 'ENST00000573202', 'translationStart': 0, 'hgvsProtein': '', 'cdsEnd': 0, 'cdnaEnd': 0, 'somatic': '0', 'distanceToTranscript': 9986, 'consequenceTypes': ['intron_variant'], 'peptideAlleleString': '', 'translationEnd': 0, 'cdsStart': 0, 'polyphenPrediction': '', 'hgvsTranscript': 'ENST00000573202.1:c.356-7090G>A', 'hgvsGenomic': '', 'alleleString': 'G/A', 'polyphenScore': 0.0, 'siftPrediction': ''}, {'siftScore': 0.0, 'cdnaStart': 0, 'codonAlleleString': '', 'transcriptId': 'ENST00000575687', 'translationStart': 0, 'hgvsProtein': '', 'cdsEnd': 0, 'cdnaEnd': 0, 'somatic': '0', 'distanceToTranscript': 1768, 'consequenceTypes': ['intron_variant'], 'peptideAlleleString': '', 'translationEnd': 0, 'cdsStart': 0, 'polyphenPrediction': '', 'hgvsTranscript': 'ENST00000575687.2:c.929-482G>A', 'hgvsGenomic': '', 'alleleString': 'G/A', 'polyphenScore': 0.0, 'siftPrediction': ''}, {'siftScore': 0.0, 'cdnaStart': 0, 'codonAlleleString': '', 'transcriptId': 'ENST00000572500', 'translationStart': 0, 'hgvsProtein': '', 'cdsEnd': 0, 'cdnaEnd': 0, 'somatic': '0', 'distanceToTranscript': 1768, 'consequenceTypes': ['intron_variant'], 'peptideAlleleString': '', 'translationEnd': 0, 'cdsStart': 0, 'polyphenPrediction': '', 'hgvsTranscript': 'ENST00000572500.2:c.*296-482G>A', 'hgvsGenomic': '', 'alleleString': 'G/A', 'polyphenScore': 0.0, 'siftPrediction': ''}], 'minorAlleleFreq': ''}
Clinical variants from databases such as ClinVar, COSMIC or GWAS catalog.
{
"properties": {
"accessionNumber": {
"type": "string"
},
"age": {
"type": "number"
},
"alternate": {
"type": "string"
},
"chromosome": {
"type": "string"
},
"comments": {
"type": "string"
},
"end": {
"type": "integer"
},
"geneCDSLength": {
"type": "integer"
},
"geneName": {
"type": "string"
},
"genomeWideScreen": {
"type": "string"
},
"hgncId": {
"type": "string"
},
"histologySubtype": {
"type": "string"
},
"idSample": {
"type": "string"
},
"idStudy": {
"type": "integer"
},
"id_tumour": {
"type": "string"
},
"mutationAA": {
"type": "string"
},
"mutationCDS": {
"type": "string"
},
"mutationDescription": {
"type": "string"
},
"mutationGRCh37GenomePosition": {
"type": "string"
},
"mutationGRCh37Strand": {
"type": "string"
},
"mutationID": {
"type": "string"
},
"mutationSomaticStatus": {
"type": "string"
},
"mutationZygosity": {
"type": "string"
},
"primaryHistology": {
"type": "string"
},
"primarySite": {
"type": "string"
},
"reference": {
"type": "string"
},
"sampleName": {
"type": "string"
},
"sampleSource": {
"type": "string"
},
"siteSubtype": {
"type": "string"
},
"snp": {
"type": "boolean"
},
"start": {
"type": "integer"
},
"tumourOrigin": {
"type": "string"
}
},
"type": "object"
}
Please, find below an example of a document stored in the gene collection. Tip: you can copy-paste the code below into a json editor to improve visualization (e.g. http://jsoneditoronline.org/):
{'histologySubtype': 'adenocarcinoma', 'reference': 'A', 'mutationGRCh37Strand': '-', 'comments': 'Stage:IIA', 'hgncId': '11548', 'sampleSource': 'NS', 'chromosome': 'X', 'geneName': 'TAF7L', 'end': 100531072, 'alternate': 'G', 'tumourOrigin': 'NS', 'id_tumour': '1566056', 'start': 100531072, 'primarySite': 'large_intestine', 'siteSubtype': 'colon', 'geneCDSLength': 1389, 'genomeWideScreen': 'y', 'primaryHistology': 'carcinoma', 'mutationGRCh37GenomePosition': '23:100531072-100531072', 'idStudy': 376, 'sampleName': 'TCGA-D5-6930-01', 'mutationCDS': 'c.1200A>G', 'snp': False, 'age': 67.0, 'idSample': '1651269', 'accessionNumber': 'ENST00000372907', 'mutationAA': 'p.K400K', 'mutationDescription': 'Substitution - coding silent', 'mutationSomaticStatus': 'Reported in another cancer sample as somatic', 'mutationID': '25490', 'mutationZygosity': 'het'}