Schema for ncbiRefSeqLink
  Database: xenTro9    Primary Table: ncbiRefSeqLink    Row Count: 43,634   Data last updated: 2021-02-11
Format description: Metadata for NCBI RefSeq tracks
On download server: MariaDB table dump directory
fieldexampleSQL type info description
id NM_001001190.1varchar(255) values id for this gene or curated item
status Provisionalvarchar(255) values Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown
name tmem178.2varchar(255) values gene name
product transmembrane protein 178, ...varchar(255) values product
mrnaAcc NM_001001190.1varchar(255) values transcript_id
protAcc NP_001001190.1varchar(255) values protein_id
locusLinkId 407851varchar(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_001001190.1varchar(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 tmem178bvarchar(255) values list of synonym names
ncrna_class  varchar(255) values type of RNA: miRNA, lncRNA, snoRNA, etc...
note The RefSeq transcript has 6...longblob   other notes from genbank record
description  longblob   description from rna gbff record via gbProcess
externalId XB-GENE-5809007varchar(255) values for outside URL link, WormBase, FlyBase, RGD, SGD, etc... from Dbxref

Connected Tables and Joining Fields
        xenTro9.ncbiRefSeq.name (via ncbiRefSeqLink.id)
      xenTro9.ncbiRefSeqCds.id (via ncbiRefSeqLink.id)
      xenTro9.ncbiRefSeqCurated.name (via ncbiRefSeqLink.id)
      xenTro9.ncbiRefSeqPredicted.name (via ncbiRefSeqLink.id)
      xenTro9.ncbiRefSeqPsl.qName (via ncbiRefSeqLink.id)
      xenTro9.seqNcbiRefSeq.acc (via ncbiRefSeqLink.id)
      xenTro9.ncbiRefSeqPepTable.name (via ncbiRefSeqLink.protAcc)

Sample Rows
 
idstatusnameproductmrnaAccprotAcclocusLinkIdomimIdhgncgenbankpseudogbkeysourcegene_biotypegene_synonymncrna_classnotedescriptionexternalId
NM_001001190.1Provisionaltmem178.2transmembrane protein 178, gene 2NM_001001190.1NP_001001190.1407851NM_001001190.1mRNABestRefSeqprotein_codingtmem178bThe RefSeq transcript has 6 substitutions and aligns at 96% coverage compared to this genomic sequenceXB-GENE-5809007
NM_001001191.1Provisionaldhrs9dehydrogenase/reductase (SDR family) member 9NM_001001191.1NP_001001191.1407852NM_001001191.1mRNABestRefSeqprotein_coding3alpha-hsd,rdh15,rdhl,retsdr8The RefSeq transcript has 1 substitution compared to this genomic sequenceXB-GENE-973205
NM_001001196.1Provisionalcited2Cbp/p300-interacting transactivator, with Glu/Asp rich carboxy-terminal domain, 2NM_001001196.1NP_001001196.1407853NM_001001196.1mRNABestRefSeqprotein_codingmrg1,p35srjThe RefSeq transcript has 4 non-frameshifting indels compared to this genomic sequenceXB-GENE-495035
NM_001001197.1Provisionalpdha1pyruvate dehydrogenase (lipoamide) alpha 1, transcript variant 1NM_001001197.1NP_001001197.1549826NM_001001197.1mRNABestRefSeqprotein_codingpdha,pdha1-a,pdha1-b,pdhce1a,phe1aThe RefSeq transcript has 8 substitutions, 2 non-frameshifting indels compared to this genomic sequenceXB-GENE-952669
NM_001001198.1Provisionalsnrpbsmall nuclear ribonucleoprotein polypeptides B and B1NM_001001198.1NP_001001198.1407857NM_001001198.1mRNABestRefSeqprotein_codingcod,sm-b/b',smb/b',smb/smb',snrnp-b,snrpb1,snurfXB-GENE-5877283
NM_001001199.1Provisionalxbp1X-box binding protein 1NM_001001199.1NP_001001199.1407858NM_001001199.1mRNABestRefSeqprotein_codingtreb5,xbp2,xXBP1The RefSeq transcript has 1 substitution compared to this genomic sequenceXB-GENE-487124
NM_001001200.1Provisionalgalnt7polypeptide N-acetylgalactosaminyltransferase 7NM_001001200.1NP_001001200.1407859NM_001001200.1mRNABestRefSeqprotein_codingThe RefSeq transcript has 1 substitution, 1 non-frameshifting indel compared to this genomic sequenceXB-GENE-950785
NM_001001202.1Provisionalstt3aSTT3A, subunit of the oligosaccharyltransferase complex (catalytic)NM_001001202.1NP_001001202.1407861NM_001001202.1mRNABestRefSeqprotein_codingXB-GENE-973638
NM_001001204.1Provisionalfam188afamily with sequence similarity 188 member ANM_001001204.1NP_001001204.1407862NM_001001204.1mRNABestRefSeqprotein_codingcarpThe RefSeq transcript has 3 substitutions, 1 non-frameshifting indel compared to this genomic sequenceXB-GENE-957056
NM_001001205.1Provisionallrrc59leucine rich repeat containing 59NM_001001205.1NP_001001205.1407863NM_001001205.1mRNABestRefSeqprotein_codingThe RefSeq transcript has 6 substitutions, 5 non-frameshifting indels compared to this genomic sequenceXB-GENE-963187

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