VIT vitrin [Homo sapiens (human)] - Gene

Summary

Official Symbol: VITprovided by HGNC
Official Full Name: vitrinprovided by HGNC
Primary source: HGNC:HGNC:12697
See related: Ensembl:ENSG00000205221 MIM:617693; AllianceGenome:HGNC:12697
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: VIT1
Summary: This gene encodes an extracellular matrix (ECM) protein. The protein may be associated with cell adhesion and migration. High levels of expression of the protein in specific parts of the brain suggest its likely role in neural development. [provided by RefSeq, Jun 2016]
Expression: Biased expression in ovary (RPKM 7.8), fat (RPKM 5.2) and 10 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p22.2

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (36696707..36814794)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (36703628..36821971)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (36923850..37041937)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH45772 (e-PCR)
- UniSTS:47379

SHGC-57668 (e-PCR)
- UniSTS:20565

SHGC-172307 (e-PCR)
- UniSTS:182128

RH68949 (e-PCR)
- UniSTS:80334

G60201 (e-PCR)
- UniSTS:137460

D6S1558 (e-PCR)
- UniSTS:49653

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables glycosaminoglycan binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell-substrate adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in spinal cord development	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in interstitial matrix	IBA Inferred from Biological aspect of Ancestor 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.

Genomic

NG_050963.1 RefSeqGene

Range

5023..123110

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001177969.2 → NP_001171440.1 vitrin isoform 2 precursor

See identical proteins and their annotated locations for NP_001171440.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.

Source sequence(s)

AC007363, AK056772, AY358338, CD679226

Consensus CDS

CCDS54347.1

UniProtKB/Swiss-Prot

A1A526, A6NKI9, A8K7Y4, E9PF47, Q6P7T3, Q6UXI7, Q96DM8, Q96DT1, Q9UDN0

UniProtKB/TrEMBL

B5MD45

Related

ENSP00000374625.3, ENST00000389975.7

Conserved Domains (3) summary

cd01472
Location:494 → 654

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:44 → 133

LCCL; LCCL domain

cl00057
Location:293 → 456

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_001177970.2 → NP_001171441.1 vitrin isoform 3 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two exons in the coding region compared to variant 1. The resulting protein (isoform 3) is shorter but has the same N- and C-termini compared to isoform 1.

Source sequence(s)

AC007363, AK056772, BC128260, CD679226

Consensus CDS

CCDS54348.1

UniProtKB/TrEMBL

B5MD45

Related

ENSP00000385658.1, ENST00000401530.5

Conserved Domains (3) summary

cd01472
Location:473 → 633

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:44 → 133

LCCL; LCCL domain

cl00057
Location:272 → 435

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_001177971.2 → NP_001171442.1 vitrin isoform 4 precursor

See identical proteins and their annotated locations for NP_001171442.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two exons in the coding region compared to variant 1. The resulting protein (isoform 4) is shorter but has the same N- and C-termini compared to isoform 1.

Source sequence(s)

AC007363, AF063833, AK056772, CD679226

Consensus CDS

CCDS54349.1

UniProtKB/TrEMBL

B5MD45

Related

ENSP00000368543.3, ENST00000379241.7

Conserved Domains (3) summary

cd01472
Location:472 → 632

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:44 → 133

LCCL; LCCL domain

cl00057
Location:271 → 434

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_001177972.3 → NP_001171443.1 vitrin isoform 5 precursor

See identical proteins and their annotated locations for NP_001171443.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) contains an alternate segment at its 3' end compared to variant 1. The resulting protein (isoform 5) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC007363

Consensus CDS

CCDS54350.1

UniProtKB/Swiss-Prot

Q6UXI7

Related

ENSP00000393561.2, ENST00000457137.6

Conserved Domains (1) summary

pfam03815
Location:44 → 133

LCCL; LCCL domain
NM_001328661.2 → NP_001315590.1 vitrin isoform 6 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 6, which lacks an internal segment and is shorter, compared to isoform 1.

Source sequence(s)

AC007363, BU726492

UniProtKB/TrEMBL

B5MD45

Related

ENSP00000384154.1, ENST00000404084.5
NM_001391966.1 → NP_001378895.1 vitrin isoform 7 precursor

Status: REVIEWED

Source sequence(s)

AC007363

UniProtKB/TrEMBL

B5MD45

Conserved Domains (3) summary

cd01472
Location:445 → 605

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:44 → 133

LCCL; LCCL domain

cl00057
Location:244 → 407

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_001391967.1 → NP_001378896.1 vitrin isoform 8 precursor

Status: REVIEWED

Source sequence(s)

AC007363

UniProtKB/TrEMBL

B5MD45

Conserved Domains (3) summary

cd01472
Location:445 → 604

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:44 → 133

LCCL; LCCL domain

cl00057
Location:244 → 407

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_001391968.1 → NP_001378897.1 vitrin isoform 9 precursor

Status: REVIEWED

Source sequence(s)

AC007363

UniProtKB/TrEMBL

B5MD45

Conserved Domains (3) summary

cd01472
Location:430 → 590

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:44 → 133

LCCL; LCCL domain

cl00057
Location:229 → 392

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_001391969.1 → NP_001378898.1 vitrin isoform 10 precursor

Status: REVIEWED

Source sequence(s)

AC007363

UniProtKB/TrEMBL

B5MD45

Conserved Domains (3) summary

cd01472
Location:423 → 583

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:44 → 133

LCCL; LCCL domain

cl00057
Location:222 → 385

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_001391970.1 → NP_001378899.1 vitrin isoform 11 precursor

Status: REVIEWED

Source sequence(s)

AC007363

Conserved Domains (1) summary

pfam03815
Location:44 → 133

LCCL; LCCL domain
NM_053276.4 → NP_444506.2 vitrin isoform 1 precursor

See identical proteins and their annotated locations for NP_444506.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the shortest isoform (1).

Source sequence(s)

AC007363, AK056772, CD679226

Consensus CDS

CCDS33180.1

UniProtKB/TrEMBL

B5MD45

Related

ENSP00000368544.3, ENST00000379242.8

Conserved Domains (3) summary

cd01472
Location:509 → 669

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:44 → 133

LCCL; LCCL domain

cl00057
Location:308 → 471

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

36696707..36814794

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011532906.3 → XP_011531208.1 vitrin isoform X1

UniProtKB/TrEMBL

B5MD45

Conserved Domains (3) summary

cd01472
Location:408 → 568

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:44 → 133

LCCL; LCCL domain

cl00057
Location:207 → 370

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
XM_017004327.2 → XP_016859816.1 vitrin isoform X2
XM_017004328.2 → XP_016859817.1 vitrin isoform X3
XM_047444749.1 → XP_047300705.1 vitrin isoform X4

UniProtKB/TrEMBL

C9J6F5

Related

ENSP00000417874.1, ENST00000497382.5