Schema for ncbiRefSeqLink
  Database: panTro6    Primary Table: ncbiRefSeqLink    Row Count: 102,467   Data last updated: 2020-04-01
Format description: Metadata for NCBI RefSeq tracks
On download server: MariaDB table dump directory
fieldexampleSQL type info description
id NM_001008975.1varchar(255) values id for this gene or curated item
status Provisionalvarchar(255) values Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown
name KDM5Dvarchar(255) values gene name
product lysine demethylase 5Dvarchar(255) values product
mrnaAcc NM_001008975.1varchar(255) values transcript_id
protAcc NP_001008975.1varchar(255) values protein_id
locusLinkId 449032varchar(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_001008975.1varchar(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 JARID1D,SMCYvarchar(255) values list of synonym names
ncrna_class  varchar(255) values type of RNA: miRNA, lncRNA, snoRNA, etc...
note The RefSeq transcript has 3...longblob   other notes from genbank record
description  longblob   description from rna gbff record via gbProcess
externalId  varchar(255) values for outside URL link, WormBase, FlyBase, RGD, SGD, etc... from Dbxref

Connected Tables and Joining Fields
        panTro6.ncbiRefSeq.name (via ncbiRefSeqLink.id)
      panTro6.ncbiRefSeqCds.id (via ncbiRefSeqLink.id)
      panTro6.ncbiRefSeqCurated.name (via ncbiRefSeqLink.id)
      panTro6.ncbiRefSeqPredicted.name (via ncbiRefSeqLink.id)
      panTro6.ncbiRefSeqPsl.qName (via ncbiRefSeqLink.id)
      panTro6.seqNcbiRefSeq.acc (via ncbiRefSeqLink.id)
      panTro6.ncbiRefSeqPepTable.name (via ncbiRefSeqLink.protAcc)

Sample Rows
 
idstatusnameproductmrnaAccprotAcclocusLinkIdomimIdhgncgenbankpseudogbkeysourcegene_biotypegene_synonymncrna_classnotedescriptionexternalId
NM_001008975.1ProvisionalKDM5Dlysine demethylase 5DNM_001008975.1NP_001008975.1449032NM_001008975.1mRNABestRefSeqprotein_codingJARID1D,SMCYThe RefSeq transcript has 3 substitutions compared to this genomic sequence
NM_001008976.1ProvisionalAPOA2apolipoprotein A2NM_001008976.1NP_001008976.1449498NM_001008976.1mRNABestRefSeqprotein_codingThe RefSeq transcript has 1 substitution compared to this genomic sequence
NM_001008977.1ProvisionalEIF1AYeukaryotic translation initiation factor 1A, Y-linkedNM_001008977.1NP_001008977.1449499NM_001008977.1mRNABestRefSeqprotein_coding
NM_001008978.1ProvisionalFUT9fucosyltransferase 9NM_001008978.1NP_001008978.1449500NM_001008978.1mRNABestRefSeqprotein_coding
NM_001008979.1ProvisionalLILRB1leukocyte immunoglobulin like receptor B1NM_001008979.1NP_001008979.1449501NM_001008979.1mRNABestRefSeqprotein_codingLIRaThe RefSeq transcript has 50 substitutions, 2 non-frameshifting indels compared to this genomic sequence
NM_001008980.1ProvisionalLILRB2leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2NM_001008980.1NP_001008980.1449502NM_001008980.1mRNABestRefSeqprotein_codingLIRbThe RefSeq transcript has 8 substitutions compared to this genomic sequence
NM_001008982.1ProvisionalPOFUT1protein O-fucosyltransferase 1NM_001008982.1NP_001008982.1449504NM_001008982.1mRNABestRefSeqprotein_codingfut12
NM_001008983.1ProvisionalPOFUT2protein O-fucosyltransferase 2NM_001008983.1NP_001008983.1449505NM_001008983.1mRNABestRefSeqprotein_codingfut13The RefSeq transcript has 4 substitutions compared to this genomic sequence
NM_001008984.1ProvisionalFUT8fucosyltransferase 8NM_001008984.1NP_001008984.1449506NM_001008984.1mRNABestRefSeqprotein_coding
NM_001008985.2ProvisionalFUT4fucosyltransferase 4NM_001008985.2NP_001008985.2449507NM_001008985.2mRNABestRefSeqprotein_coding

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