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    VIT vitrin [ Homo sapiens (human) ]

    Gene ID: 5212, updated on 6-Jun-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
    mouse all
    NEW
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    Try the new Transcript table

    Genomic context

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    See VIT in Genome Data Viewer
    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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    NEW Try the new Transcript table

    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

      UniProtKB/TrEMBL
      B5MD45

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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