Schema for ncbiRefSeqLink
  Database: xenLae2    Primary Table: ncbiRefSeqLink    Row Count: 60,920   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_001085445.1varchar(255) values id for this gene or curated item
status Validatedvarchar(255) values Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown
name shfm1.Svarchar(255) values gene name
product split hand/foot malformatio...varchar(255) values product
mrnaAcc NM_001085445.1varchar(255) values transcript_id
protAcc NP_001078914.1varchar(255) values protein_id
locusLinkId 447126varchar(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_001085445.1varchar(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 dss1,ecd,sem1,shfd1,shfdg1,...varchar(255) values list of synonym names
ncrna_class  varchar(255) values type of RNA: miRNA, lncRNA, snoRNA, etc...
note The RefSeq transcript has 2...longblob   other notes from genbank record
description  longblob   description from rna gbff record via gbProcess
externalId XB-GENE-1016356varchar(255) values for outside URL link, WormBase, FlyBase, RGD, SGD, etc... from Dbxref

Connected Tables and Joining Fields
        xenLae2.ncbiRefSeq.name (via ncbiRefSeqLink.id)
      xenLae2.ncbiRefSeqCds.id (via ncbiRefSeqLink.id)
      xenLae2.ncbiRefSeqCurated.name (via ncbiRefSeqLink.id)
      xenLae2.ncbiRefSeqPredicted.name (via ncbiRefSeqLink.id)
      xenLae2.ncbiRefSeqPsl.qName (via ncbiRefSeqLink.id)
      xenLae2.seqNcbiRefSeq.acc (via ncbiRefSeqLink.id)
      xenLae2.ncbiRefSeqPepTable.name (via ncbiRefSeqLink.protAcc)

Sample Rows
 
idstatusnameproductmrnaAccprotAcclocusLinkIdomimIdhgncgenbankpseudogbkeysourcegene_biotypegene_synonymncrna_classnotedescriptionexternalId
NM_001085445.1Validatedshfm1.Ssplit hand/foot malformation (ectrodactyly) type 1 S homeologNM_001085445.1NP_001078914.1447126NM_001085445.1mRNABestRefSeqprotein_codingdss1,ecd,sem1,shfd1,shfdg1,shfm1,shsf1The RefSeq transcript has 2 substitutions, 2 non-frameshifting indels compared to this genomic sequenceXB-GENE-1016356
NM_001085482.1Provisionalbdnf.Sbrain-derived neurotrophic factor S homeologNM_001085482.1NP_001078951.1100048914NM_001085482.1mRNABestRefSeqprotein_codingbdnf,bdnf-a,bdnf-bThe RefSeq transcript aligns at 5% coverage compared to this genomic sequenceXB-GENE-955559
NM_001085483.1Provisionaldmrt1.Sdoublesex and mab-3 related transcription factor 1 S homeologNM_001085483.1NP_001078952.1100048915NM_001085483.1mRNABestRefSeqprotein_codingdmrt1-a,dmrt1-b,dmrt1-beta,dmt1,xdmrt1The RefSeq transcript has 3 substitutions compared to this genomic sequenceXB-GENE-6255833
NM_001085484.1Provisionalpor.LP450 (cytochrome) oxidoreductase L homeologNM_001085484.1NP_001078953.1379707NM_001085484.1mRNABestRefSeqprotein_codingnpr,por,xporThe RefSeq transcript has 39 substitutions, 6 non-frameshifting indels and aligns at 99% coverage compared to this genomic seque ...XB-GENE-951366
NM_001085556.1Provisionalslc5a11.Lsolute carrier family 5 (sodium/inositol cotransporter), member 11 L homeologNM_001085556.1NP_001079025.1373547NM_001085556.1mRNABestRefSeqprotein_codingSGLT-1-like,sglt-1-like-a,SGLT-1L,slc5a11The RefSeq transcript has 10 substitutions, 3 non-frameshifting indels compared to this genomic sequenceXB-GENE-1010722
NM_001085557.1Provisionalfoxd3.Lforkhead box D3 L homeologNM_001085557.1NP_001079026.1373548NM_001085557.1mRNABestRefSeqprotein_codingfkh6,foxd3,foxd3-a,foxd3-b,XFD-6,xfoxd3The RefSeq transcript has 1 substitution, 1 non-frameshifting indel and aligns at 96% coverage compared to this genomic sequenceXB-GENE-865691
NM_001085558.1ProvisionalLOC100487918.Lcytochrome P450 4B1-like L homeologNM_001085558.1NP_001079027.1373549NM_001085558.1mRNABestRefSeqprotein_codingcypxl301-aThe RefSeq transcript has 22 substitutions, 2 non-frameshifting indels compared to this genomic sequenceXB-GENE-980017
NM_001085559.1Provisionalt2.ST, brachyury homolog, gene 2 S homeologNM_001085559.1NP_001079028.1373550NM_001085559.1mRNABestRefSeqprotein_codingbra3-a,t2,Xbra3The RefSeq transcript aligns at 41% coverage compared to this genomic sequenceXB-GENE-5981788
NM_001085560.1Provisionalmet.LMET proto-oncogene, receptor tyrosine kinase L homeologNM_001085560.1NP_001079029.1373551NM_001085560.1mRNABestRefSeqprotein_codingc-met,met,met-AThe RefSeq transcript has 28 substitutions and aligns at 99% coverage compared to this genomic sequenceXB-GENE-865462
NM_001085561.1Provisionalcrb2.Scrumbs family member 2 S homeologNM_001085561.1NP_001079030.1373552NM_001085561.1mRNABestRefSeqprotein_codingcrb2,erl-a,XerlThe RefSeq transcript has 6 substitutions, 2 non-frameshifting indels compared to this genomic sequenceXB-GENE-6078472

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