Schema for ncbiRefSeqLink
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Database: xenLae2 Primary Table: ncbiRefSeqLink Row Count: 60,920   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_001085445.1 | varchar(255) | values | id for this gene or curated item |
status | Validated | varchar(255) | values | Inferred, Model, Predicted, Provisional, Reviewed, Validated, Unknown |
name | shfm1.S | varchar(255) | values | gene name |
product | split hand/foot malformatio... | varchar(255) | values | product |
mrnaAcc | NM_001085445.1 | varchar(255) | values | transcript_id |
protAcc | NP_001078914.1 | varchar(255) | values | protein_id |
locusLinkId | 447126 | 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_001085445.1 | 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 | dss1,ecd,sem1,shfd1,shfdg1,... | varchar(255) | values | list of synonym names |
ncrna_class | | varchar(255) | values | type of RNA: miRNA, lncRNA, snoRNA, etc... |
note | The RefSeq transcript has 2... | longblob | | other notes from genbank record |
description | | longblob | | description from rna gbff record via gbProcess |
externalId | XB-GENE-1016356 | 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_001085445.1 | Validated | shfm1.S | split hand/foot malformation (ectrodactyly) type 1 S homeolog | NM_001085445.1 | NP_001078914.1 | 447126 | | | NM_001085445.1 | | mRNA | BestRefSeq | protein_coding | dss1,ecd,sem1,shfd1,shfdg1,shfm1,shsf1 | | The RefSeq transcript has 2 substitutions, 2 non-frameshifting indels compared to this genomic sequence | | XB-GENE-1016356 |
NM_001085482.1 | Provisional | bdnf.S | brain-derived neurotrophic factor S homeolog | NM_001085482.1 | NP_001078951.1 | 100048914 | | | NM_001085482.1 | | mRNA | BestRefSeq | protein_coding | bdnf,bdnf-a,bdnf-b | | The RefSeq transcript aligns at 5% coverage compared to this genomic sequence | | XB-GENE-955559 |
NM_001085483.1 | Provisional | dmrt1.S | doublesex and mab-3 related transcription factor 1 S homeolog | NM_001085483.1 | NP_001078952.1 | 100048915 | | | NM_001085483.1 | | mRNA | BestRefSeq | protein_coding | dmrt1-a,dmrt1-b,dmrt1-beta,dmt1,xdmrt1 | | The RefSeq transcript has 3 substitutions compared to this genomic sequence | | XB-GENE-6255833 |
NM_001085484.1 | Provisional | por.L | P450 (cytochrome) oxidoreductase L homeolog | NM_001085484.1 | NP_001078953.1 | 379707 | | | NM_001085484.1 | | mRNA | BestRefSeq | protein_coding | npr,por,xpor | | The RefSeq transcript has 39 substitutions, 6 non-frameshifting indels and aligns at 99% coverage compared to this genomic seque ... | | XB-GENE-951366 |
NM_001085556.1 | Provisional | slc5a11.L | solute carrier family 5 (sodium/inositol cotransporter), member 11 L homeolog | NM_001085556.1 | NP_001079025.1 | 373547 | | | NM_001085556.1 | | mRNA | BestRefSeq | protein_coding | SGLT-1-like,sglt-1-like-a,SGLT-1L,slc5a11 | | The RefSeq transcript has 10 substitutions, 3 non-frameshifting indels compared to this genomic sequence | | XB-GENE-1010722 |
NM_001085557.1 | Provisional | foxd3.L | forkhead box D3 L homeolog | NM_001085557.1 | NP_001079026.1 | 373548 | | | NM_001085557.1 | | mRNA | BestRefSeq | protein_coding | fkh6,foxd3,foxd3-a,foxd3-b,XFD-6,xfoxd3 | | The RefSeq transcript has 1 substitution, 1 non-frameshifting indel and aligns at 96% coverage compared to this genomic sequence | | XB-GENE-865691 |
NM_001085558.1 | Provisional | LOC100487918.L | cytochrome P450 4B1-like L homeolog | NM_001085558.1 | NP_001079027.1 | 373549 | | | NM_001085558.1 | | mRNA | BestRefSeq | protein_coding | cypxl301-a | | The RefSeq transcript has 22 substitutions, 2 non-frameshifting indels compared to this genomic sequence | | XB-GENE-980017 |
NM_001085559.1 | Provisional | t2.S | T, brachyury homolog, gene 2 S homeolog | NM_001085559.1 | NP_001079028.1 | 373550 | | | NM_001085559.1 | | mRNA | BestRefSeq | protein_coding | bra3-a,t2,Xbra3 | | The RefSeq transcript aligns at 41% coverage compared to this genomic sequence | | XB-GENE-5981788 |
NM_001085560.1 | Provisional | met.L | MET proto-oncogene, receptor tyrosine kinase L homeolog | NM_001085560.1 | NP_001079029.1 | 373551 | | | NM_001085560.1 | | mRNA | BestRefSeq | protein_coding | c-met,met,met-A | | The RefSeq transcript has 28 substitutions and aligns at 99% coverage compared to this genomic sequence | | XB-GENE-865462 |
NM_001085561.1 | Provisional | crb2.S | crumbs family member 2 S homeolog | NM_001085561.1 | NP_001079030.1 | 373552 | | | NM_001085561.1 | | mRNA | BestRefSeq | protein_coding | crb2,erl-a,Xerl | | The RefSeq transcript has 6 substitutions, 2 non-frameshifting indels compared to this genomic sequence | | XB-GENE-6078472 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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