RGD GENES_xxx readme file. Last updated - February 2017 contact: rgd.developers@mcw.edu GENERAL INFORMATION: GENES_xxx files contain up-to-date information for rat, mouse and human genes found in RGD database. Genomic positions are provided for both the current and the previous reference assemblies, as well as for Celera alternate assembly. Leftmost columns are in common for both files. Last columns contain species-specific information. GENES_xxx files are in tab delimited format. Within a tab delimited field multiple values are now separated by a semicolon ";" instead of a comma "," or bar "|". This is to improve rendering of the files when viewed in Excel. MAIN CHANGES (compared with previous version): - Removed GDB_ID column. - Genomic positions are now given for reference assemblies specific for given species. - GENES_MOUSE provides information about MGD IDs and cM positions. - GENES_HUMAN provides information about HPRD IDs, HGNC IDs and OMIM IDs. - RATMAP_ID and RHDB_ID columns for RAT are discontinued -- blanks will be used for compatibility. CHANGES: Mar-11-2020 - added VGNC_ID column for DOG and PIG. - added Ensembl primary assembly positions for all species. Feb-15-2017 - HPRD IDs are discontinued for human genes -- blanks will be used for compatibility. Oct-02-2014 - added columns with Rnor_5.0 and Rnor_6.0 positions to GENES_RAT.txt file; GENES_RAT_5.0.txt and GENES_RAT_6.0 files discontinued added columns with assembly build 36 positions to GENES_MOUSE.txt file; GENES_MOUSE_B36.txt file discontinued added columns with assembly build 38 positions to GENES_HUMAN.txt file; GENES_HUMAN_B38.txt file discontinued Aug-26-2014 - generation of file GENES_RAT_6.0.txt with positions on assemblies build 6.0 and 5.0; GENES_RAT.txt and GENES_RAT_5.0 files unchanged Aug-26-2014 - generation of file GENES_HUMAN_B38.txt with positions on assemblies build 38 and 37; GENES_HUMAN.txt file unchanged Oct-11-2013 - initial release of file GENES_OBSOLETE_IDS.txt Aug-19-2013 - gene descriptions in the files will match descriptions from gene report pages Jul-06-2012 - generation of file GENES_RAT_5.0.txt with positions on assemblies build 3.4 and 5.0 GENES_RAT.txt file still unchanged, with positions on assemblies build 3.1 and 3.4 Jun-26-2012 - generation of file GENES_MOUSE_B36.txt with positions on assemblies build 36 and 37 GENES_MOUSE.txt has positions on assemblies build 37 and 38 Mar-12-2012 - added generation of file GENES_MOUSE_B38.txt with positions on assemblies build 37 and 38 Dec-20-2011 - no visible changes (fixed file headers, improved internal QC) Apr-15-2011 - added column GENE_REFSEQ_STATUS for all species Apr-01-2011 - RATMAP_ID and RHDB_ID columns are discontinued -- they will be filled with blanks for compatibility Mar-02-2011 - fixed the bug so OLD_SYMBOL column is now populated properly COLUMN INFORMATION: First 38 columns in common between rat, mouse and human. 1 GENE_RGD_ID the RGD_ID of the gene 2 SYMBOL official gene symbol 3 NAME gene name 4 GENE_DESC gene description (if available) 5 CHROMOSOME_CELERA chromosome for Celera assembly 6 CHROMOSOME_[oldAssembly#] chromosome for the old reference assembly 7 CHROMOSOME_[newAssembly#] chromosome for the current reference assembly 8 FISH_BAND fish band information 9 START_POS_CELERA start position for Celera assembly 10 STOP_POS_CELERA stop position for Celera assembly 11 STRAND_CELERA strand information for Celera assembly 12 START_POS_[oldAssembly#] start position for old reference assembly 13 STOP_POS_[oldAssembly#] stop position for old reference assembly 14 STRAND_[oldAssembly#] strand information for old reference assembly 15 START_POS_[newAssembly#] start position for current reference assembly 16 STOP_POS_[newAssembly#] stop position for current reference assembly 17 STRAND_[newAssembly#] strand information for current reference assembly 18 CURATED_REF_RGD_ID RGD_ID of paper(s) on gene 19 CURATED_REF_PUBMED_ID PUBMED_ID of paper(s) on gene 20 UNCURATED_PUBMED_ID other PUBMED ids 21 NCBI_GENE_ID NCBI Gene Id 22 UNIPROT_ID UniProtKB id(s) 23 UNCURATED_REF_MEDLINE_ID 24 GENBANK_NUCLEOTIDE GenBank Nucleotide ID(s) 25 TIGR_ID TIGR ID(s) 26 GENBANK_PROTEIN GenBank Protein ID(s) 27 UNIGENE_ID UniGene ID(s) 28 MARKER_RGD_ID RGD_ID(s) of markers associated with given gene 29 MARKER_SYMBOL marker symbol 30 OLD_SYMBOL old symbol alias(es) 31 OLD_NAME old name alias(es) 32 QTL_RGD_ID RGD_ID(s) of QTLs associated with given gene 33 QTL_SYMBOL QTL symbol 34 NOMENCLATURE_STATUS nomenclature status 35 SPLICE_RGD_ID RGD_IDs for gene splices 36 SPLICE_SYMBOL 37 GENE_TYPE gene type 38 ENSEMBL_ID Ensembl Gene ID RAT SPECIFIC COLUMNS: 39 GENE_REFSEQ_STATUS NCBI gene RefSeq Status 40 CHROMOSOME_5.0 chromosome for Rnor_5.0 reference assembly 41 START_POS_5.0 start position for Rnor_5.0 reference assembly 42 STOP_POS_5.0 stop position for Rnor_5.0 reference assembly 43 STRAND_5.0 strand information for Rnor_5.0 reference assembly 44 CHROMOSOME_6.0 chromosome for Rnor_6.0 reference assembly 45 START_POS_6.0 start position for Rnor_6.0 reference assembly 46 STOP_POS_6.0 stop position for Rnor_6.0 reference assembly 47 STRAND_6.0 strand information for Rnor_6.0 reference assembly HUMAN SPECIFIC COLUMNS: 39 HGNC_ID HGNC ID 40 (UNUSED) 41 OMIM_ID OMIM ID 42 GENE_REFSEQ_STATUS NCBI gene RefSeq Status 43 CHROMOSOME_38 chromosome for GRCh38 reference assembly 44 START_POS_38 start position for GRCh38 reference assembly 45 STOP_POS_38 stop position for GRCh38 reference assembly 46 STRAND_38 strand information for GRCh38 reference assembly MOUSE SPECIFIC COLUMNS: 39 MGD_ID MGD ID 40 CM_POS mouse cM map absolute position 41 GENE_REFSEQ_STATUS NCBI gene RefSeq Status 42 CHROMOSOME_36 chromosome for reference assembly build 36 43 START_POS_36 start position for reference assembly build 36 44 STOP_POS_36 stop position for reference assembly build 36 45 STRAND_36 strand information for reference assembly build 36 GENES_OBSOLETE_IDS.txt ---------------------- GENES_OBSOLETE_IDS.txt contains a list of the genes in the RGD database which have been either WITHDRAWN or RETIRED (designated as "OLD_GENE" in the list). In RGD, a gene is "WITHDRAWN" when the record is no longer active and has not been replaced by or merged into another gene record. A gene is "RETIRED" when the gene has been merged into another record so that the second record (i.e. the "NEW_GENE") is considered "a replacement for" or "equivalent to" the retired one. In some cases, the "NEW_GENE" may have subsequently also been retired or withdrawn, in which case a second line where this is designated as the "OLD_GENE" will also appear in the file. An example appears below the list of column headers. This file is updated approximately weekly to reflect an up-to-date list of the obsoletions. Columns in the GENES_OBSOLETE_IDS.txt are as follows: #COLUMN INFORMATION: #1 SPECIES name of the species #2 OLD_GENE_RGD_ID old gene RGD ID #3 OLD_GENE_SYMBOL old gene symbol #4 OLD_GENE_STATUS old gene status #5 OLD_GENE_TYPE old gene type #6 NEW_GENE_RGD_ID new gene RGD ID (if any) #7 NEW_GENE_SYMBOL new gene symbol (if any) #8 NEW_GENE_STATUS old gene status (if any) #9 NEW_GENE_TYPE new gene type (if any) Example lines: WITHDRAWN GENE: rat 2005 A39_mapped WITHDRAWN mapped RETIRED GENE: rat 2008 Abl1_mapped RETIRED mapped 1584969 Abl1 ACTIVE protein-coding NEW_GENE SUBSEQUENTLY WITHDRAWN: rat 2105 Amd3 RETIRED gene 2106 Amd-ps_mapped WITHDRAWN mapped rat 2106 Amd-ps_mapped WITHDRAWN mapped GENES_ALLELES.txt and GENES_SPLICES.txt --------------------------------------- The GENES_RAT.txt file does not contain information about gene alleles or splice variants. These records can be found in the GENES_ALLELES.txt and GENES_SPLICES.txt files, respectively. Columns in these files contain headers, indicating the type of data in each column. These files contain map data for all three currently used rat genome assemblies, RGSC 3.4, 5.0 and 6.0, but unlike records in the GENES_RAT.txt, each row in the allele or splice file contains only one map position with the assembly specified in column 9 (i.e. for a gene allele which maps to all three assemblies, there will be three rows in the GENES_ALLELES.txt file: a row containing the v3.4 position of the gene, a row for the v5.0 position and a row for the v6.0 position, with all other data the same between those rows.)