Schema for ncbiRefSeqLink
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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
field | example | SQL type | info | description |
id | NM_001001130.3 | varchar(255) | values | id for this gene or curated item |
status | Validated | varchar(255) | values | Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown |
name | Zfp85 | varchar(255) | values | gene name |
product | zinc finger protein 85 | varchar(255) | values | product |
mrnaAcc | NM_001001130.3 | varchar(255) | values | transcript_id |
protAcc | NP_001001130.1 | varchar(255) | values | protein_id |
locusLinkId | 22746 | 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_001001130.3 | 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 | KRAB19,Rslcan2,Zfp71,Zfp85-rs1 | varchar(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:107767 | 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_001001130.3 | Validated | Zfp85 | zinc finger protein 85 | NM_001001130.3 | NP_001001130.1 | 22746 | | | NM_001001130.3 | | mRNA | BestRefSeq | protein_coding | KRAB19,Rslcan2,Zfp71,Zfp85-rs1 | | | | MGI:107767 |
NM_001001144.3 | Validated | Scap | SREBF chaperone, transcript variant 1 | NM_001001144.3 | NP_001001144.2 | 235623 | | | NM_001001144.3 | | mRNA | BestRefSeq | protein_coding | 9530044G19,mKIAA0199 | | | | MGI:2135958 |
NM_001001152.2 | Validated | Zfp458 | zinc finger protein 458, transcript variant 1 | NM_001001152.2 | NP_001001152.1 | 238690 | | | NM_001001152.2 | | mRNA | BestRefSeq | protein_coding | Gm33446,mszf59-2,Rslcan-7,Znf728 | | | | MGI:3040691 |
NM_001001160.3 | Validated | Fbxo41 | F-box protein 41, transcript variant 1 | NM_001001160.3 | NP_001001160.1 | 330369 | | | NM_001001160.3 | | mRNA | BestRefSeq | protein_coding | 9630017H13,D6Ertd538e | | | | MGI:1261912 |
NM_001001176.2 | Validated | Taf9b | TATA-box binding protein associated factor 9B, transcript variant 2 | NM_001001176.2 | NP_001001176.2 | 407786 | | | NM_001001176.2 | | mRNA | BestRefSeq | protein_coding | Taf9l | | isoform 2 is encoded by transcript variant 2 | | MGI:3039562 |
NM_001001177.2 | Validated | Tsbp1 | testis expressed basic protein 1, transcript variant 1 | NM_001001177.2 | NP_001001177.2 | 407788 | | | NM_001001177.2 | | mRNA | BestRefSeq | protein_coding | NG8,Tesb,Tesbp,TSBP | | isoform 1 is encoded by transcript variant 1 | | MGI:3039565 |
NM_001001178.2 | Validated | Ccdc148 | coiled-coil domain containing 148, transcript variant 2 | NM_001001178.2 | NP_001001178.1 | 227933 | | | NM_001001178.2 | | mRNA | BestRefSeq | protein_coding | 5830402J09,Gm38473 | | isoform 2 is encoded by transcript variant 2 | | MGI:3039583 |
NM_001001179.3 | Validated | A2ml1 | alpha-2-macroglobulin like 1 | NM_001001179.3 | NP_001001179.2 | 232400 | | | NM_001001179.3 | | mRNA | BestRefSeq | protein_coding | Ovos,Ovos2 | | | | MGI:3039594 |
NM_001001180.2 | Validated | Zfp941 | zinc finger protein 941 | NM_001001180.2 | NP_001001180.2 | 407812 | | | NM_001001180.2 | | mRNA | BestRefSeq | protein_coding | | | | | MGI:3039601 |
NM_001001181.4 | Validated | BC031181 | cDNA sequence BC031181, transcript variant 1 | NM_001001181.4 | NP_001001181.1 | 407819 | | | NM_001001181.4 | | mRNA | BestRefSeq | protein_coding | | | isoform 1 is encoded by transcript variant 1 | | MGI:3039614 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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