Schema for ncbiRefSeqLink |
|---|
| |
Database: sorAra2 Primary Table: ncbiRefSeqLink Row Count: 23,525 Data last updated: 2020-04-01
Format description: Metadata for NCBI RefSeq tracks
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
|---|
| id | NM_001280678.1 | varchar(255) | values | id for this gene or curated item |
| status | Provisional | varchar(255) | values | Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown |
| name | TTR | varchar(255) | values | gene name |
| product | transthyretin | varchar(255) | values | product |
| mrnaAcc | NM_001280678.1 | varchar(255) | values | transcript_id |
| protAcc | NP_001267607.1 | varchar(255) | values | protein_id |
| locusLinkId | 101549714 | 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_001280678.1 | 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 | Prealbumin,TRR | varchar(255) | values | list of synonym names |
| ncrna_class | | varchar(255) | values | type of RNA: miRNA, lncRNA, snoRNA, etc... |
| note | The RefSeq transcript has 8... | longblob | | other notes from genbank record |
| description | | longblob | | description from rna gbff record via gbProcess |
| externalId | | varchar(255) | values | for outside URL link, WormBase, FlyBase, RGD, SGD, etc... from Dbxref |
|
| |
|
|
|
Connected Tables and Joining Fields
|
|
|
Sample Rows
|
|---|
| |
| id | status | name | product | mrnaAcc | protAcc | locusLinkId | omimId | hgnc | genbank | pseudo | gbkey | source | gene_biotype | gene_synonym | ncrna_class | note | description | externalId |
|---|
| NM_001280678.1 | Provisional | TTR | transthyretin | NM_001280678.1 | NP_001267607.1 | 101549714 | | | NM_001280678.1 | | mRNA | BestRefSeq | protein_coding | Prealbumin,TRR | | The RefSeq transcript has 8 substitutions compared to this genomic sequence | | |
| NM_001281925.1 | Validated | TVP23B | Golgi apparatus membrane protein TVP23 homolog B | NM_001281925.1 | NP_001268854.1 | 101539834 | | | NM_001281925.1 | | mRNA | BestRefSeq | protein_coding | | | | | |
| NM_001285876.1 | Validated | RNASEH1 | ribonuclease H1 | NM_001285876.1 | NP_001272805.1 | 101558507 | | | NM_001285876.1 | | mRNA | BestRefSeq | protein_coding | | | | | |
| NM_001286187.1 | Inferred | TAF9 | TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa | NM_001286187.1 | NP_001273116.1 | 101543028 | | | NM_001286187.1 | | mRNA | BestRefSeq | protein_coding | | | | | |
| NM_001290408.1 | Reviewed | OAZ3 | ornithine decarboxylase antizyme 3 | NM_001290408.1 | NP_001277337.1 | 101537587 | | | NM_001290408.1 | | mRNA | BestRefSeq | protein_coding | | | protein translation is dependent on polyamine-induced +1 ribosomal frameshift; non-AUG (CUG) translation initiation codon | The protein encoded by this gene belongs to the ornithine decarboxylase antizyme family, which plays a role in cell growth and p ... | |
| NM_001291139.1 | Reviewed | PEG10 | paternally expressed 10, transcript variant 1 | NM_001291139.1 | NP_001278068.1 | 101550818 | | | NM_001291139.1 | | mRNA | BestRefSeq | protein_coding | | | protein translation is dependent on -1 ribosomal frameshift; isoform 1 is encoded by transcript variant 1 | This gene is thought to have been derived from the Ty3/Gypsy family of retrotransposons. It contains two overlapping open readin ... | |
| NM_001291140.1 | Reviewed | PEG10 | paternally expressed 10, transcript variant 1 | NM_001291140.1 | NP_001278069.1 | 101550818 | | | NM_001291140.1 | | mRNA | BestRefSeq | protein_coding | | | isoform 2 is encoded by transcript variant 1 | This gene is thought to have been derived from the Ty3/Gypsy family of retrotransposons. It contains two overlapping open readin ... | |
| NM_001291520.1 | Reviewed | AZIN1 | antizyme inhibitor 1, transcript variant 1 | NM_001291520.1 | NP_001278449.1 | 101548658 | | | NM_001291520.1 | | mRNA | BestRefSeq | protein_coding | | | | The protein encoded by this gene belongs to the antizyme inhibitor family, which plays a role in cell growth and proliferation b ... | |
| NM_001293736.1 | Reviewed | AZIN2 | antizyme inhibitor 2 | NM_001293736.1 | NP_001280665.1 | 101541364 | | | NM_001293736.1 | | mRNA | BestRefSeq | protein_coding | ADC | | | The protein encoded by this gene belongs to the antizyme inhibitor family, which plays a role in cell growth and proliferation b ... | |
| NM_001301748.1 | Reviewed | AZIN1 | antizyme inhibitor 1, transcript variant 2 | NM_001301748.1 | NP_001288677.1 | 101548658 | | | NM_001301748.1 | | mRNA | BestRefSeq | protein_coding | | | | The protein encoded by this gene belongs to the antizyme inhibitor family, which plays a role in cell growth and proliferation b ... | |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|
US Server