Schema for ncbiRefSeqLink |
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Database: hg38 Primary Table: ncbiRefSeqLink Row Count: 185,367 Data last updated: 2024-09-11
Format description: Metadata for NCBI RefSeq tracks
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| id | NM_000014.6 | varchar(255) | values | id for this gene or curated item |
| status | Reviewed | varchar(255) | values | Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown |
| name | A2M | varchar(255) | values | gene name |
| product | alpha-2-macroglobulin, tran... | varchar(255) | values | product |
| mrnaAcc | NM_000014.6 | varchar(255) | values | transcript_id |
| protAcc | NP_000005.3 | varchar(255) | values | protein_id |
| locusLinkId | 2 | varchar(255) | values | locus link identifier, from Dbxref |
| omimId | 103950 | varchar(255) | values | OMIM identifier, from Dbxref |
| hgnc | 7 | varchar(255) | values | HGNC identifier, from Dbxref |
| genbank | NM_000014.6 | 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 | A2MD,CPAMD5,FWP007,S863-7 | varchar(255) | values | list of synonym names |
| ncrna_class | | varchar(255) | values | type of RNA: miRNA, lncRNA, snoRNA, etc... |
| note | isoform a precursor is enco... | longblob | | other notes from genbank record |
| description | The protein encoded by this... | longblob | | description from rna gbff record via gbProcess |
| externalId | | 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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hg38.ncbiRefSeq.name (via ncbiRefSeqLink.id)
hg38.ncbiRefSeqCds.id (via ncbiRefSeqLink.id)
hg38.ncbiRefSeqCurated.name (via ncbiRefSeqLink.id)
hg38.ncbiRefSeqHgmd.name (via ncbiRefSeqLink.id)
hg38.ncbiRefSeqPredicted.name (via ncbiRefSeqLink.id)
hg38.ncbiRefSeqPsl.qName (via ncbiRefSeqLink.id)
hg38.ncbiRefSeqSelect.name (via ncbiRefSeqLink.id)
hg38.seqNcbiRefSeq.acc (via ncbiRefSeqLink.id)
hg38.omim2gene.omimId (via ncbiRefSeqLink.omimId) Note: genome-wide queries are not available for this table.
hg38.omimGene2.name (via ncbiRefSeqLink.omimId) Note: genome-wide queries are not available for this table.
hg38.omimGeneMap.omimId (via ncbiRefSeqLink.omimId) Note: genome-wide queries are not available for this table.
hg38.omimGeneMap2.omimId (via ncbiRefSeqLink.omimId) Note: genome-wide queries are not available for this table.
hg38.omimPhenotype.omimId (via ncbiRefSeqLink.omimId) Note: genome-wide queries are not available for this table.
hgFixed.refLink.omimId (via ncbiRefSeqLink.omimId)
hg38.ncbiRefSeqPepTable.name (via ncbiRefSeqLink.protAcc)
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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_000014.6 | Reviewed | A2M | alpha-2-macroglobulin, transcript variant 1 | NM_000014.6 | NP_000005.3 | 2 | 103950 | 7 | NM_000014.6 | | mRNA | BestRefSeq | protein_coding | A2MD,CPAMD5,FWP007,S863-7 | | isoform a precursor is encoded by transcript variant 1 | The protein encoded by this gene is a protease inhibitor and cytokine transporter. It uses a bait-and-trap mechanism to inhibit ... | |
| NM_000015.3 | Reviewed | NAT2 | N-acetyltransferase 2 | NM_000015.3 | NP_000006.2 | 10 | 612182 | 7646 | NM_000015.3 | | mRNA | BestRefSeq | protein_coding | AAC2,NAT-2,PNAT | | | This gene encodes an enzyme that functions to both activate and deactivate arylamine and hydrazine drugs and carcinogens. Polymo ... | |
| NM_000016.6 | Reviewed | ACADM | acyl-CoA dehydrogenase medium chain, transcript variant 1 | NM_000016.6 | NP_000007.1 | 34 | 607008 | 89 | NM_000016.6 | | mRNA | BestRefSeq | protein_coding | ACAD1,MCAD,MCADH | | isoform a precursor is encoded by transcript variant 1 | This gene encodes the medium-chain specific (C4 to C12 straight chain) acyl-Coenzyme A dehydrogenase. The homotetramer enzyme ca ... | |
| NM_000017.4 | Reviewed | ACADS | acyl-CoA dehydrogenase short chain, transcript variant 1 | NM_000017.4 | NP_000008.1 | 35 | 606885 | 90 | NM_000017.4 | | mRNA | BestRefSeq | protein_coding | ACAD3,SCAD | | isoform 1 precursor is encoded by transcript variant 1 | This gene encodes a tetrameric mitochondrial flavoprotein, which is a member of the acyl-CoA dehydrogenase family. This enzyme c ... | |
| NM_000018.4 | Reviewed | ACADVL | acyl-CoA dehydrogenase very long chain, transcript variant 1 | NM_000018.4 | NP_000009.1 | 37 | 609575 | 92 | NM_000018.4 | | mRNA | BestRefSeq | protein_coding | ACAD6,LCACD,VLCAD | | isoform 1 precursor is encoded by transcript variant 1 | The protein encoded by this gene is targeted to the inner mitochondrial membrane where it catalyzes the first step of the mitoch ... | |
| NM_000019.4 | Reviewed | ACAT1 | acetyl-CoA acetyltransferase 1, transcript variant 2 | NM_000019.4 | NP_000010.1 | 38 | 607809 | 93 | NM_000019.4 | | mRNA | BestRefSeq | protein_coding | ACAT,MAT,T2,THIL | | isoform b precursor is encoded by transcript variant 2 | This gene encodes a mitochondrially localized enzyme that catalyzes the reversible formation of acetoacetyl-CoA from two molecul ... | |
| NM_000020.3 | Reviewed | ACVRL1 | activin A receptor like type 1, transcript variant 1 | NM_000020.3 | NP_000011.2 | 94 | 601284 | 175 | NM_000020.3 | | mRNA | BestRefSeq | protein_coding | ACVRLK1,ALK-1,ALK1,HHT,HHT2,ORW2,SKR3,TSR-I | | isoform 1 precursor is encoded by transcript variant 1 | This gene encodes a type I cell-surface receptor for the TGF-beta superfamily of ligands. It shares with other type I receptors ... | |
| NM_000021.4 | Reviewed | PSEN1 | presenilin 1, transcript variant 1 | NM_000021.4 | NP_000012.1 | 5663 | 104311 | 9508 | NM_000021.4 | | mRNA | BestRefSeq | protein_coding | ACNINV3,AD3,FAD,PS-1,PS1,PSNL1,S182 | | isoform I-467 is encoded by transcript variant 1 | Alzheimer's disease (AD) patients with an inherited form of the disease carry mutations in the presenilin proteins (PSEN1; PSEN2 ... | |
| NM_000022.4 | Reviewed | ADA | adenosine deaminase, transcript variant 1 | NM_000022.4 | NP_000013.2 | 100 | 608958 | 186 | NM_000022.4 | | mRNA | BestRefSeq | protein_coding | ADA1 | | isoform 1 is encoded by transcript variant 1 | This gene encodes an enzyme that catalyzes the hydrolysis of adenosine to inosine in the purine catabolic pathway. Various mutat ... | |
| NM_000023.4 | Reviewed | SGCA | sarcoglycan alpha, transcript variant 1 | NM_000023.4 | NP_000014.1 | 6442 | 600119 | 10805 | NM_000023.4 | | mRNA | BestRefSeq | protein_coding | 50DAG,adhalin,ADL,DAG2,DMDA2,LGMD2D,LGMDR3,SCARMD1 | | isoform 1 precursor is encoded by transcript variant 1 | This gene encodes a component of the dystrophin-glycoprotein complex (DGC), which is critical to the stability of muscle fiber m ... | |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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US Server