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VIT vitrin [ Homo sapiens (human) ]

Gene ID: 5212, updated on 4-Jun-2020

Summary

Official Symbol
VITprovided by HGNC
Official Full Name
vitrinprovided by HGNC
Primary source
HGNC:HGNC:12697
See related
Ensembl:ENSG00000205221 MIM:617693
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

Genomic context

See VIT in Genome Data Viewer
Location:
2p22.2
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (36696690..36814794)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (36923833..37041937)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene receptor for activated C kinase 1 pseudogene Neighboring gene Sharpr-MPRA regulatory region 2322 Neighboring gene striatin Neighboring gene RNA, U6 small nuclear 577, pseudogene Neighboring gene HEAT repeat containing 5B

Genomic regions, transcripts, and products

Expression

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC70561, MGC149746, DKFZp313L1517

Gene Ontology Provided by GOA

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

NCBI Reference Sequences (RefSeq)

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_001177969.1NP_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
    Q6UXI7
    Related
    ENSP00000374625.3, ENST00000389975.7
    Conserved Domains (3) summary
    cd01472
    Location:494654
    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:44133
    LCCL; LCCL domain
    cl00057
    Location:293456
    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_001177970.2NP_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/Swiss-Prot
    Q6UXI7
    Related
    ENSP00000385658.1, ENST00000401530.5
    Conserved Domains (3) summary
    cd01472
    Location:473633
    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:44133
    LCCL; LCCL domain
    cl00057
    Location:272435
    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_001177971.2NP_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/Swiss-Prot
    Q6UXI7
    Related
    ENSP00000368543.3, ENST00000379241.7
    Conserved Domains (3) summary
    cd01472
    Location:472632
    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:44133
    LCCL; LCCL domain
    cl00057
    Location:271434
    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_001177972.2NP_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, AK292149, BC061519
    Consensus CDS
    CCDS54350.1
    UniProtKB/Swiss-Prot
    Q6UXI7
    Related
    ENSP00000393561.2, ENST00000457137.6
    Conserved Domains (1) summary
    pfam03815
    Location:44133
    LCCL; LCCL domain
  5. NM_001328661.2NP_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
    Related
    ENSP00000384154.1, ENST00000404084.5
  6. NM_053276.4NP_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/Swiss-Prot
    Q6UXI7
    Related
    ENSP00000368544.3, ENST00000379242.7
    Conserved Domains (3) summary
    cd01472
    Location:509669
    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:44133
    LCCL; LCCL domain
    cl00057
    Location:308471
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    36696690..36814794
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532905.2XP_011531207.1  vitrin isoform X1

    Conserved Domains (3) summary
    cd01472
    Location:445605
    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:44133
    LCCL; LCCL domain
    cl00057
    Location:244407
    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_017004326.2XP_016859815.1  vitrin isoform X2

  3. XM_011532906.2XP_011531208.1  vitrin isoform X3

    Conserved Domains (3) summary
    cd01472
    Location:408568
    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:44133
    LCCL; LCCL domain
    cl00057
    Location:207370
    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. XM_017004327.1XP_016859816.1  vitrin isoform X4

  5. XM_017004328.1XP_016859817.1  vitrin isoform X5

    Related
    ENSP00000417874.1, ENST00000497382.5
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