Index of /monthly_releases/2026/pombase-2026-06-01/gene_names_and_identifiers

 Name                                       Last modified      Size  Description
 Parent Directory                                                -   
 gene_IDs_names_products.tsv                2026-06-01 02:00  1.3M  
 gene_ids_and_details.parquet               2026-06-01 02:00  8.4M  

This directory contains files of S. pombe genes IDs, names and other attributes.

gene_IDs_names_products.tsv -
  This file is composed of 8 columns:
    - gene_systematic_id: PomBase systematic identifier (eg. SPAC1039.10)
    - gene_systematic_id_with_prefix: systematic ID with prefix
        (eg. PomBase:SPAC1039.10)
    - gene_name: main gene symbol (eg. mmf2)
    - chromosome_id: chromosome on which the gene is located (eg. chromosome_1)
    - gene_product: description of the gene product
        (eg. mitochondrial matrix protein, YjgF family protein Mmf2,
         reactive intermediate)
    - uniprot_id: UniProt accession number, for protein-coding genes only
        (eg. Q9UR06)
    - gene_type: PomBase feature type (eg. protein coding gene)
    - synonyms: other gene names used in the literature (eg. hpm1,SPAC922.01)

gene_ids_and_details.parquet -
  This file (in Parquet format) contains all information from the file above
  and also includes most details from available from PomBase gene page.
  There is one row per gene.
  Annotation data available in other files is not included, examples:
  GO, phenotype and interaction annotation

  Columns:
    systematic_id - PomBase systematic identifier (eg. SPAC1039.10)
    name - main gene symbol (eg. mmf2) - if any
    taxonid - always 4896
    product - description of the gene product
    deletion_viability - one of "inviable", "viable", "depends_on_conditions" and
                         "unknown"
                         See this FAQ for more:
                         https://www.pombase.org/faq/why-are-some-genes-annotated-both-viable-and-inviable-phenotypes
    uniprot_identifier - UniProt accession for protein-coding genes (eg. Q9UR06)
    interpro_matches - details of InterPro domain matches for this gene
    tm_domain_coords - coordinates of trans-membrane domains (if any)
    low_complexity_region_coords - coordinates of low complexity regions
    schizosaccharomyces_orthogroup - The ID of the Schizosaccharomyces orthogroup
                                     that contains this gene (if any)
                                     See: https://www.sogweb.org/
    synonyms - gene synonyms and type ("obsolete_name" or "exact")
    dbxrefs - IDs for this gene in selected other databases
    orthologs - human, S. cerevisiae and S. japonicus orthologs (if any)
    feature_type - One of "snoRNA gene", "rRNA gene", "pseudogene", "snRNA gene",
                   "tRNA gene", "lncRNA gene", "protein", "sncRNA gene"
    transcript_so_termid - a term from the Sequence Ontology describing the
                           type of the transcript, example: SO:0000252 "rRNA"
    characterisation_status - See: https://www.pombase.org/faq/what-does-characterisation-status-mean-gene
                              and https://www.pombase.org/status/protein-status-tracker
                              for information
    taxonomic_distribution - See: https://www.pombase.org/documentation/taxonomic-conservation
    location - the chromosome ID, start, end and strand of this gene
    transcripts - details of the transcript and protein IDs, locations and
                  sequence
                  also includes protein attributes such as molecular weight
    biogrid_interactor_id - The BioGRID ID of this gene
    name_descriptions -
    gocams - the IDs and names of any GO-CAM pathways that include this gene
    coiled_coil_coords - the coordinates of any coiled coils
    pdb_entries - the IDs and other details of any available PDB structures
                  for this gene

This directory is part of PomBase release 2026-06-01

For use of this dataset please cite:
  Pascal Carme, Kim Rutherford, Jürg Bähler, Juan Mata, Valerie Wood
  PomBase in 2026: Expanding Knowledge, Modelling Connections
  Genetics, January 2026
  https://doi.org/10.1093/genetics/iyag001