Schema for ncbiRefSeqLink
  Database: mm39    Primary Table: ncbiRefSeqLink    Row Count: 136,259   Data last updated: 2024-02-20
Format description: Metadata for NCBI RefSeq tracks
On download server: MariaDB table dump directory
fieldexampleSQL type info description
id NM_001001130.3varchar(255) values id for this gene or curated item
status Validatedvarchar(255) values Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown
name Zfp85varchar(255) values gene name
product zinc finger protein 85varchar(255) values product
mrnaAcc NM_001001130.3varchar(255) values transcript_id
protAcc NP_001001130.1varchar(255) values protein_id
locusLinkId 22746varchar(255) values locus link identifier, from Dbxref
omimId  varchar(255) values OMIM identifier, from Dbxref
hgnc  varchar(255) values HGNC identifier, from Dbxref
genbank NM_001001130.3varchar(255) values genbank identifier from Dbxref
pseudo  varchar(255) values 'true' if pseudo gene, or n/a
gbkey mRNAvarchar(255) values genbank key: Gene, mRNA, ncRNA, rRNA, tRNA, etc...
source BestRefSeqvarchar(255) values source: RefSeq, tRNAscan-SE, Gnomon, Curated Genomic, BestRefSeq
gene_biotype protein_codingvarchar(255) values bio type: protein_coding, pseudogene, C_region, J_segment_pseudogene, other
gene_synonym KRAB19,Rslcan2,Zfp71,Zfp85-rs1varchar(255) values list of synonym names
ncrna_class  varchar(255) values type of RNA: miRNA, lncRNA, snoRNA, etc...
note  longblob   other notes from genbank record
description  longblob   description from rna gbff record via gbProcess
externalId MGI:107767varchar(255) values for outside URL link, WormBase, FlyBase, RGD, SGD, etc... from Dbxref

Connected Tables and Joining Fields
        mm39.ncbiRefSeq.name (via ncbiRefSeqLink.id)
      mm39.ncbiRefSeqCds.id (via ncbiRefSeqLink.id)
      mm39.ncbiRefSeqCurated.name (via ncbiRefSeqLink.id)
      mm39.ncbiRefSeqPredicted.name (via ncbiRefSeqLink.id)
      mm39.ncbiRefSeqPsl.qName (via ncbiRefSeqLink.id)
      mm39.ncbiRefSeqSelect.name (via ncbiRefSeqLink.id)
      mm39.seqNcbiRefSeq.acc (via ncbiRefSeqLink.id)
      mm39.ncbiRefSeqPepTable.name (via ncbiRefSeqLink.protAcc)

Sample Rows
 
idstatusnameproductmrnaAccprotAcclocusLinkIdomimIdhgncgenbankpseudogbkeysourcegene_biotypegene_synonymncrna_classnotedescriptionexternalId
NM_001001130.3ValidatedZfp85zinc finger protein 85NM_001001130.3NP_001001130.122746NM_001001130.3mRNABestRefSeqprotein_codingKRAB19,Rslcan2,Zfp71,Zfp85-rs1MGI:107767
NM_001001144.3ValidatedScapSREBF chaperone, transcript variant 1NM_001001144.3NP_001001144.2235623NM_001001144.3mRNABestRefSeqprotein_coding9530044G19,mKIAA0199MGI:2135958
NM_001001152.2ValidatedZfp458zinc finger protein 458, transcript variant 1NM_001001152.2NP_001001152.1238690NM_001001152.2mRNABestRefSeqprotein_codingGm33446,mszf59-2,Rslcan-7,Znf728MGI:3040691
NM_001001160.3ValidatedFbxo41F-box protein 41, transcript variant 1NM_001001160.3NP_001001160.1330369NM_001001160.3mRNABestRefSeqprotein_coding9630017H13,D6Ertd538eMGI:1261912
NM_001001176.2ValidatedTaf9bTATA-box binding protein associated factor 9B, transcript variant 2NM_001001176.2NP_001001176.2407786NM_001001176.2mRNABestRefSeqprotein_codingTaf9lisoform 2 is encoded by transcript variant 2MGI:3039562
NM_001001177.2ValidatedTsbp1testis expressed basic protein 1, transcript variant 1NM_001001177.2NP_001001177.2407788NM_001001177.2mRNABestRefSeqprotein_codingNG8,Tesb,Tesbp,TSBPisoform 1 is encoded by transcript variant 1MGI:3039565
NM_001001178.2ValidatedCcdc148coiled-coil domain containing 148, transcript variant 2NM_001001178.2NP_001001178.1227933NM_001001178.2mRNABestRefSeqprotein_coding5830402J09,Gm38473isoform 2 is encoded by transcript variant 2MGI:3039583
NM_001001179.3ValidatedA2ml1alpha-2-macroglobulin like 1NM_001001179.3NP_001001179.2232400NM_001001179.3mRNABestRefSeqprotein_codingOvos,Ovos2MGI:3039594
NM_001001180.2ValidatedZfp941zinc finger protein 941NM_001001180.2NP_001001180.2407812NM_001001180.2mRNABestRefSeqprotein_codingMGI:3039601
NM_001001181.4ValidatedBC031181cDNA sequence BC031181, transcript variant 1NM_001001181.4NP_001001181.1407819NM_001001181.4mRNABestRefSeqprotein_codingisoform 1 is encoded by transcript variant 1MGI:3039614

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.