Schema for ncbiRefSeqLink
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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
field | example | SQL type | info | description |
id | NM_001001190.1 | varchar(255) | values | id for this gene or curated item |
status | Provisional | varchar(255) | values | Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown |
name | tmem178.2 | varchar(255) | values | gene name |
product | transmembrane protein 178, ... | varchar(255) | values | product |
mrnaAcc | NM_001001190.1 | varchar(255) | values | transcript_id |
protAcc | NP_001001190.1 | varchar(255) | values | protein_id |
locusLinkId | 407851 | varchar(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_001001190.1 | varchar(255) | values | genbank identifier from Dbxref |
pseudo | | varchar(255) | values | 'true' if pseudo gene, or n/a |
gbkey | mRNA | varchar(255) | values | genbank key: Gene, mRNA, ncRNA, rRNA, tRNA, etc... |
source | BestRefSeq | varchar(255) | values | source: RefSeq, tRNAscan-SE, Gnomon, Curated Genomic, BestRefSeq |
gene_biotype | protein_coding | varchar(255) | values | bio type: protein_coding, pseudogene, C_region, J_segment_pseudogene, other |
gene_synonym | tmem178b | varchar(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-5809007 | varchar(255) | values | for outside URL link, WormBase, FlyBase, RGD, SGD, etc... from Dbxref |
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Connected Tables and Joining Fields
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Sample Rows
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id | status | name | product | mrnaAcc | protAcc | locusLinkId | omimId | hgnc | genbank | pseudo | gbkey | source | gene_biotype | gene_synonym | ncrna_class | note | description | externalId |
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NM_001001190.1 | Provisional | tmem178.2 | transmembrane protein 178, gene 2 | NM_001001190.1 | NP_001001190.1 | 407851 | | | NM_001001190.1 | | mRNA | BestRefSeq | protein_coding | tmem178b | | The RefSeq transcript has 6 substitutions and aligns at 96% coverage compared to this genomic sequence | | XB-GENE-5809007 |
NM_001001191.1 | Provisional | dhrs9 | dehydrogenase/reductase (SDR family) member 9 | NM_001001191.1 | NP_001001191.1 | 407852 | | | NM_001001191.1 | | mRNA | BestRefSeq | protein_coding | 3alpha-hsd,rdh15,rdhl,retsdr8 | | The RefSeq transcript has 1 substitution compared to this genomic sequence | | XB-GENE-973205 |
NM_001001196.1 | Provisional | cited2 | Cbp/p300-interacting transactivator, with Glu/Asp rich carboxy-terminal domain, 2 | NM_001001196.1 | NP_001001196.1 | 407853 | | | NM_001001196.1 | | mRNA | BestRefSeq | protein_coding | mrg1,p35srj | | The RefSeq transcript has 4 non-frameshifting indels compared to this genomic sequence | | XB-GENE-495035 |
NM_001001197.1 | Provisional | pdha1 | pyruvate dehydrogenase (lipoamide) alpha 1, transcript variant 1 | NM_001001197.1 | NP_001001197.1 | 549826 | | | NM_001001197.1 | | mRNA | BestRefSeq | protein_coding | pdha,pdha1-a,pdha1-b,pdhce1a,phe1a | | The RefSeq transcript has 8 substitutions, 2 non-frameshifting indels compared to this genomic sequence | | XB-GENE-952669 |
NM_001001198.1 | Provisional | snrpb | small nuclear ribonucleoprotein polypeptides B and B1 | NM_001001198.1 | NP_001001198.1 | 407857 | | | NM_001001198.1 | | mRNA | BestRefSeq | protein_coding | cod,sm-b/b',smb/b',smb/smb',snrnp-b,snrpb1,snurf | | | | XB-GENE-5877283 |
NM_001001199.1 | Provisional | xbp1 | X-box binding protein 1 | NM_001001199.1 | NP_001001199.1 | 407858 | | | NM_001001199.1 | | mRNA | BestRefSeq | protein_coding | treb5,xbp2,xXBP1 | | The RefSeq transcript has 1 substitution compared to this genomic sequence | | XB-GENE-487124 |
NM_001001200.1 | Provisional | galnt7 | polypeptide N-acetylgalactosaminyltransferase 7 | NM_001001200.1 | NP_001001200.1 | 407859 | | | NM_001001200.1 | | mRNA | BestRefSeq | protein_coding | | | The RefSeq transcript has 1 substitution, 1 non-frameshifting indel compared to this genomic sequence | | XB-GENE-950785 |
NM_001001202.1 | Provisional | stt3a | STT3A, subunit of the oligosaccharyltransferase complex (catalytic) | NM_001001202.1 | NP_001001202.1 | 407861 | | | NM_001001202.1 | | mRNA | BestRefSeq | protein_coding | | | | | XB-GENE-973638 |
NM_001001204.1 | Provisional | fam188a | family with sequence similarity 188 member A | NM_001001204.1 | NP_001001204.1 | 407862 | | | NM_001001204.1 | | mRNA | BestRefSeq | protein_coding | carp | | The RefSeq transcript has 3 substitutions, 1 non-frameshifting indel compared to this genomic sequence | | XB-GENE-957056 |
NM_001001205.1 | Provisional | lrrc59 | leucine rich repeat containing 59 | NM_001001205.1 | NP_001001205.1 | 407863 | | | NM_001001205.1 | | mRNA | BestRefSeq | protein_coding | | | The RefSeq transcript has 6 substitutions, 5 non-frameshifting indels compared to this genomic sequence | | XB-GENE-963187 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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