InterMine data files

Data files for PombeMine

pombemine_gene_details

Location: https://curation.pombase.org/dumps/latest_build/intermine_data/pombemine_gene_details.gz

Contains an array of gene details.

Fields for each gene

• name - gene name
• systematic_id - PomBase systematic gene ID
• synonyms - an array of { "name": "...", "type": "..." }
  • the type can be "exact" or "obsolete_name"
• product
• feature_type - one of:
  • mRNA gene
  • pseudogene
  • ncRNA gene
  • rRNA gene
  • snoRNA gene
  • snRNA gene
  • tRNA gene
• location - the start, end and chromosome of the feature
• uniprot_identifier
• taxonid - always 4896
• transcripts - an array of transcript details:
  • uniquename - derived from the uniquename of the gene
  • location - start, end, strand and chromosome of the transcript, including UTRs
  • cds_location - location not including UTR, only written for coding genes
  • transcript_type - one of:
    • mRNA
    • ncRNA
    • pseudogenic_transcript
    • rRNA
    • snoRNA
    • snRNA
    • tRNA
  • protein - only for coding genes. Contents:
    • uniquename
    • sequence
    • protein stats
  • parts - an array of:
    • uniquename - derived from the uniquename of the gene
    • feature_type - one of:
      • cds_intron
      • exon
      • five_prime_utr
      • five_prime_utr_intron
      • three_prime_utr
      • three_prime_utr_intron
    • location - chromosome location of this exon/intron/utr
• references - the references for the annotations, location and orthologs of this gene

Example

[
  {
    "name": "mrx11",
    "synonyms": [
      {
        "name": "SPAC1610.05",
        "type": "exact"
      }
    ],
    "product": "mitochondrial expression network (MIOREX) component Mrx11",
    "systematic_id": "SPAC1002.01",
    "feature_type": "mRNA gene",
    "location": {
      "chromosome_name": "chromosome_1",
      "start_pos": 1798347,
      "end_pos": 1799015,
      "strand": "forward"
    },
    "transcripts": [
      {
        "uniquename": "SPAC1002.01.1",
        "location": {
          "chromosome_name": "chromosome_1",
          "start_pos": 1798347,
          "end_pos": 1799015,
          "strand": "forward"
        },
        "parts": [
          {
            "feature_type": "exon",
            "uniquename": "SPAC1002.01.1:exon:1",
            "name": null,
            "location": {
              "chromosome_name": "chromosome_1",
              "start_pos": 1798347,
              "end_pos": 1798830,
              "strand": "forward",
              "phase": "0"
            },
            "residues": "ATGTTACCAC..."
          },
          {
            "feature_type": "cds_intron",
            "uniquename": "SPAC1002.01.1:intron:1",
            "name": null,
            "location": {
              "chromosome_name": "chromosome_1",
              "start_pos": 1798831,
              "end_pos": 1798959,
              "strand": "forward"
            },
            "residues": "GTTAGTATAAATCGC..."
          },
          {
            "feature_type": "exon",
            "uniquename": "SPAC1002.01.1:exon:2",
            "name": null,
            "location": {
              "chromosome_name": "chromosome_1",
              "start_pos": 1798960,
              "end_pos": 1799015,
              "strand": "forward",
              "phase": "0"
            },
            "residues": "CTTATTTTGT..."
          }
        ],
        "transcript_type": "mRNA",
        "protein": {
          "uniquename": "SPAC1002.01.1:pep",
          "sequence": "MLPPTIRISGLAKT...",
          "product": "mitochondrial expression network (MIOREX) component Mrx11",
          "molecular_weight": 20.2386,
          "average_residue_weight": 0.11243,
          "charge_at_ph7": 14.9,
          "isoelectric_point": 10.77,
          "codon_adaptation_index": 0.57
        },
        "cds_location": {
          "chromosome_name": "chromosome_1",
          "start_pos": 1798347,
          "end_pos": 1799015,
          "strand": "forward",
          "phase": "0"
        }
      }
    ],
    "uniprot_identifier": "Q9US57",
    "taxonid": 4896
  }
]