Schema for ncbiRefSeqLink
|
|
Database: panTro6 Primary Table: ncbiRefSeqLink Row Count: 102,467   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_001008975.1 | varchar(255) | values | id for this gene or curated item |
status | Provisional | varchar(255) | values | Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown |
name | KDM5D | varchar(255) | values | gene name |
product | lysine demethylase 5D | varchar(255) | values | product |
mrnaAcc | NM_001008975.1 | varchar(255) | values | transcript_id |
protAcc | NP_001008975.1 | varchar(255) | values | protein_id |
locusLinkId | 449032 | 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_001008975.1 | 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 | JARID1D,SMCY | varchar(255) | values | list of synonym names |
ncrna_class | | varchar(255) | values | type of RNA: miRNA, lncRNA, snoRNA, etc... |
note | The RefSeq transcript has 3... | 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_001008975.1 | Provisional | KDM5D | lysine demethylase 5D | NM_001008975.1 | NP_001008975.1 | 449032 | | | NM_001008975.1 | | mRNA | BestRefSeq | protein_coding | JARID1D,SMCY | | The RefSeq transcript has 3 substitutions compared to this genomic sequence | | |
NM_001008976.1 | Provisional | APOA2 | apolipoprotein A2 | NM_001008976.1 | NP_001008976.1 | 449498 | | | NM_001008976.1 | | mRNA | BestRefSeq | protein_coding | | | The RefSeq transcript has 1 substitution compared to this genomic sequence | | |
NM_001008977.1 | Provisional | EIF1AY | eukaryotic translation initiation factor 1A, Y-linked | NM_001008977.1 | NP_001008977.1 | 449499 | | | NM_001008977.1 | | mRNA | BestRefSeq | protein_coding | | | | | |
NM_001008978.1 | Provisional | FUT9 | fucosyltransferase 9 | NM_001008978.1 | NP_001008978.1 | 449500 | | | NM_001008978.1 | | mRNA | BestRefSeq | protein_coding | | | | | |
NM_001008979.1 | Provisional | LILRB1 | leukocyte immunoglobulin like receptor B1 | NM_001008979.1 | NP_001008979.1 | 449501 | | | NM_001008979.1 | | mRNA | BestRefSeq | protein_coding | LIRa | | The RefSeq transcript has 50 substitutions, 2 non-frameshifting indels compared to this genomic sequence | | |
NM_001008980.1 | Provisional | LILRB2 | leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2 | NM_001008980.1 | NP_001008980.1 | 449502 | | | NM_001008980.1 | | mRNA | BestRefSeq | protein_coding | LIRb | | The RefSeq transcript has 8 substitutions compared to this genomic sequence | | |
NM_001008982.1 | Provisional | POFUT1 | protein O-fucosyltransferase 1 | NM_001008982.1 | NP_001008982.1 | 449504 | | | NM_001008982.1 | | mRNA | BestRefSeq | protein_coding | fut12 | | | | |
NM_001008983.1 | Provisional | POFUT2 | protein O-fucosyltransferase 2 | NM_001008983.1 | NP_001008983.1 | 449505 | | | NM_001008983.1 | | mRNA | BestRefSeq | protein_coding | fut13 | | The RefSeq transcript has 4 substitutions compared to this genomic sequence | | |
NM_001008984.1 | Provisional | FUT8 | fucosyltransferase 8 | NM_001008984.1 | NP_001008984.1 | 449506 | | | NM_001008984.1 | | mRNA | BestRefSeq | protein_coding | | | | | |
NM_001008985.2 | Provisional | FUT4 | fucosyltransferase 4 | NM_001008985.2 | NP_001008985.2 | 449507 | | | NM_001008985.2 | | mRNA | BestRefSeq | protein_coding | | | | | |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|