Vit vitrin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vitprovided by RGD
Official Full Name: vitrinprovided by RGD
Primary source: RGD:1564128
See related: EnsemblRapid:ENSRNOG00000004706 AllianceGenome:RGD:1564128
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1564128
Summary: Predicted to enable glycosaminoglycan binding activity. Predicted to be involved in extracellular matrix organization; positive regulation of cell-substrate adhesion; and spinal cord development. Predicted to be located in extracellular matrix. Predicted to be active in interstitial matrix. Orthologous to human VIT (vitrin). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Muscle (RPKM 22.1), Testes (RPKM 9.5) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q12

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (22198095..22317758, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (16445966..16565644, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (1091817..1208888)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

D6Rat40 (e-PCR)
- UniSTS:119391

D6Rat80 (e-PCR)
- UniSTS:118995

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables glycosaminoglycan binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within extracellular matrix organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell-substrate adhesion	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of cell-substrate adhesion	ISO Inferred from Sequence Orthology more info
involved_in spinal cord development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
is_active_in interstitial matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in interstitial matrix	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: vitrin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001431887.1 → NP_001418816.1 vitrin precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/TrEMBL

A0A8I5ZT33, F1M095

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086024.1 Reference GRCr8

Range

22198095..22317758 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008764427.4 → XP_008762649.1 vitrin isoform X1

Related

ENSRNOP00000081700.1, ENSRNOT00000098785.2

Conserved Domains (2) summary

cd01472
Location:467 → 627

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

pfam03815
Location:45 → 134

LCCL; LCCL domain
XM_039113076.2 → XP_038969004.1 vitrin isoform X2

UniProtKB/TrEMBL

A6H9W2

Conserved Domains (1) summary

cd01472
Location:240 → 400

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...