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VIT vitrin [ Homo sapiens (human) ]

Gene ID: 5212, updated on 3-Apr-2024

Summary

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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
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Genomic context

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Location:
2p22.2
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (36696707..36814794)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (36703628..36821971)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (36923850..37041937)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:36788221-36789420 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:36824452-36825379 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:36825380-36826306 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:36827234-36828159 Neighboring gene fasciculation and elongation protein zeta 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15576 Neighboring gene Sharpr-MPRA regulatory region 2322 Neighboring gene uncharacterized LOC124905990 Neighboring gene RACK1 pseudogene 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:36964254-36964949 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:36981017-36981669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15577 Neighboring gene Sharpr-MPRA regulatory region 5815 Neighboring gene RNA, U6 small nuclear 577, pseudogene Neighboring gene striatin Neighboring gene MPRA-validated peak3656 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr2:37189639-37189834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11352 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:37230067-37230233 Neighboring gene HEAT repeat containing 5B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15578

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Common Genetic Variant in VIT Is Associated with Human Brain Asymmetry. Tadayon SH, et al. Front Hum Neurosci, 2016. PMID 27252636, Free PMC Article
  2. Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere. Whittaker CA, et al. Mol Biol Cell, 2002 Oct. PMID 12388743, Free PMC Article
  3. Gene expression profile of the human trabecular meshwork: NEIBank sequence tag analysis. Tomarev SI, et al. Invest Ophthalmol Vis Sci, 2003 Jun. PMID 12766061
  4. VIT-1: the second member of a new branch of the von Willebrand factor A domain superfamily. Mayne R, et al. Biochem Soc Trans, 1999 Dec. PMID 10830112
  5. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC70561, MGC149746, DKFZp313L1517

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

  1. NG_050963.1 RefSeqGene

    Range
    5023..123110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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 ...

  2. 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 ...

  3. 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 ...

  4. 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

  5. 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

  6. 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 ...

  7. 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 ...

  8. 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 ...

  9. 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 ...

  10. 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

  11. 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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    36696707..36814794
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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 ...

  2. XM_017004327.2 → XP_016859816.1  vitrin isoform X2

  3. XM_017004328.2 → XP_016859817.1  vitrin isoform X3

  4. XM_047444749.1 → XP_047300705.1  vitrin isoform X4

    UniProtKB/TrEMBL
    C9J6F5
    Related
    ENSP00000417874.1, ENST00000497382.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    36703628..36821971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342558.1 → XP_054198533.1  vitrin isoform X1

  2. XM_054342559.1 → XP_054198534.1  vitrin isoform X2

  3. XM_054342560.1 → XP_054198535.1  vitrin isoform X3

  4. XM_054342561.1 → XP_054198536.1  vitrin isoform X4

    UniProtKB/TrEMBL
    C9J6F5
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6UXI7.1 GenPept UniProtKB/Swiss-Prot:Q6UXI7

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