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Aliases for VIT Gene

Aliases for VIT Gene

External Ids for VIT Gene

Previous GeneCards Identifiers for VIT Gene

  • GC02P036888
  • GC02P037070
  • GC02P036898
  • GC02P036835

Summaries for VIT Gene

Entrez Gene Summary for VIT Gene

  • 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]

GeneCards Summary for VIT Gene

VIT (Vitrin) is a Protein Coding gene. GO annotations related to this gene include glycosaminoglycan binding. An important paralog of this gene is COCH.

UniProtKB/Swiss-Prot for VIT Gene

  • Promotes matrix assembly and cell adhesiveness.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VIT Gene

Genomics for VIT Gene

Regulatory Elements for VIT Gene

Enhancers for VIT Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F036753 0.7 Ensembl ENCODE 7.7 +57.4 57373 1.5 SOX13 TEAD4 ZNF644 RARA NR2F6 CREM HOMEZ SOX5 GATAD2A NFIA VIT GC02P036764 GC02P036731
GH02F036657 0.7 Ensembl ENCODE 4.4 -37.4 -37393 3.2 ATF1 MLX ZFP64 ARID4B SLC30A9 FOS ZNF202 JUNB MXD4 MIER2 ENSG00000272054 HEATR5B CEBPZ PRKD3 CRIM1 VIT LOC100422559
GH02F036481 1.1 FANTOM5 Ensembl ENCODE 1.7 -208.9 -208924 11.8 SIN3A DMAP1 FOS NFYC PPARG KAT8 SSRP1 MAFF SMARCA4 PBX2 CRIM1 FEZ2 VIT ENSG00000273090 GC02P036388
GH02F036695 0.8 ENCODE 0.8 +0.2 192 2.2 CTCF GFI1B CEBPB ZNF843 RAD21 GATA3 SMC3 FOS ZBTB33 TRIM28 VIT GC02P036731
GH02F036700 0.5 ENCODE 0.8 +5.0 4998 1.7 CTCF SMARCC1 RFX1 DPF2 ZNF592 ZNF217 CTBP1 GATA3 ZNF239 RCOR1 VIT GC02P036731
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around VIT on UCSC Golden Path with GeneCards custom track

Promoters for VIT Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000588150 410 601 ZNF843 TRIM28 TCF7L2
ENSR00001821533 1210 201 CEBPB ZNF843 TRIM28 TCF7L2

Genomic Location for VIT Gene

Chromosome:
2
Start:
36,696,690 bp from pter
End:
36,814,794 bp from pter
Size:
118,105 bases
Orientation:
Plus strand

Genomic View for VIT Gene

Genes around VIT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VIT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VIT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VIT Gene

Proteins for VIT Gene

  • Protein details for VIT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6UXI7-VITRN_HUMAN
    Recommended name:
    Vitrin
    Protein Accession:
    Q6UXI7
    Secondary Accessions:
    • A1A526
    • A6NKI9
    • A8K7Y4
    • E9PF47
    • Q6P7T3
    • Q96DM8
    • Q96DT1
    • Q9UDN0

    Protein attributes for VIT Gene

    Size:
    678 amino acids
    Molecular mass:
    73930 Da
    Quaternary structure:
    • Binds dermatan sulfate and chondroitin sulfate.

    Alternative splice isoforms for VIT Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VIT Gene

Post-translational modifications for VIT Gene

  • Glycosylation at Asn 390 and Asn 520
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VIT Gene

Domains & Families for VIT Gene

Protein Domains for VIT Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for VIT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6UXI7

UniProtKB/Swiss-Prot:

VITRN_HUMAN :
  • Contains 1 LCCL domain.
Domain:
  • Contains 1 LCCL domain.
  • Contains 2 VWFA domains.
genes like me logo Genes that share domains with VIT: view

No data available for Gene Families for VIT Gene

Function for VIT Gene

Molecular function for VIT Gene

UniProtKB/Swiss-Prot Function:
Promotes matrix assembly and cell adhesiveness.

Gene Ontology (GO) - Molecular Function for VIT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005539 glycosaminoglycan binding IEA --
genes like me logo Genes that share ontologies with VIT: view
genes like me logo Genes that share phenotypes with VIT: view

Animal Model Products

  • Taconic Biosciences Mouse Models for VIT

miRNA for VIT Gene

miRTarBase miRNAs that target VIT

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VIT Gene

Localization for VIT Gene

Subcellular locations from UniProtKB/Swiss-Prot for VIT Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VIT Gene COMPARTMENTS Subcellular localization image for VIT gene
Compartment Confidence
extracellular 3
endoplasmic reticulum 2
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for VIT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005614 interstitial matrix IEA --
genes like me logo Genes that share ontologies with VIT: view

Pathways & Interactions for VIT Gene

SuperPathways for VIT Gene

No Data Available

Interacting Proteins for VIT Gene

Selected Interacting proteins: Q6UXI7-VITRN_HUMAN for VIT Gene via IID

Symbol External ID(s) Details
ITIH5
ZNF655

Gene Ontology (GO) - Biological Process for VIT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010811 positive regulation of cell-substrate adhesion IEA --
GO:0030198 extracellular matrix organization IEA --
genes like me logo Genes that share ontologies with VIT: view

No data available for Pathways by source and SIGNOR curated interactions for VIT Gene

Transcripts for VIT Gene

Unigene Clusters for VIT Gene

Vitrin:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VIT Gene

No ASD Table

Relevant External Links for VIT Gene

GeneLoc Exon Structure for
VIT
ECgene alternative splicing isoforms for
VIT

Expression for VIT Gene

mRNA expression in normal human tissues for VIT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VIT Gene

This gene is overexpressed in Nerve - Tibial (x7.5) and Adipose - Subcutaneous (x4.6).

Protein differential expression in normal tissues from HIPED for VIT Gene

This gene is overexpressed in Prostate (19.0), Oral epithelium (9.3), Adipocyte (7.2), Spinal cord (6.7), Testis (6.5), and Gallbladder (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VIT Gene



NURSA nuclear receptor signaling pathways regulating expression of VIT Gene:

VIT

SOURCE GeneReport for Unigene cluster for VIT Gene:

Hs.137415
genes like me logo Genes that share expression patterns with VIT: view

Primer Products

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for VIT Gene

Orthologs for VIT Gene

This gene was present in the common ancestor of chordates.

Orthologs for VIT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VIT 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VIT 34 35
  • 87.83 (n)
cow
(Bos Taurus)
Mammalia VIT 34 35
  • 85.84 (n)
mouse
(Mus musculus)
Mammalia Vit 34 16 35
  • 85.18 (n)
rat
(Rattus norvegicus)
Mammalia Vit 34
  • 84.39 (n)
oppossum
(Monodelphis domestica)
Mammalia VIT 35
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VIT 35
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves VIT 34 35
  • 71.14 (n)
lizard
(Anolis carolinensis)
Reptilia VIT 35
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100489513 34
  • 66.07 (n)
zebrafish
(Danio rerio)
Actinopterygii ch1073-291c23.1 34 35
  • 64.17 (n)
Species where no ortholog for VIT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VIT Gene

ENSEMBL:
Gene Tree for VIT (if available)
TreeFam:
Gene Tree for VIT (if available)

Paralogs for VIT Gene

(5) SIMAP similar genes for VIT Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VIT: view

Variants for VIT Gene

Sequence variations from dbSNP and Humsavar for VIT Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs386352378 Uncertain significance 36,787,249(+) TGCCG(G/T)TCCAC reference, missense
rs1005100 -- 36,722,633(+) CAAAC(A/T)GAGGT intron-variant
rs1014584 -- 36,790,383(-) AAGGA(G/T)CAGAA intron-variant
rs1015695 -- 36,732,742(-) ttgcc(C/T)gttga intron-variant
rs1015696 -- 36,732,717(-) acctt(C/T)gattg intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VIT Gene

Variant ID Type Subtype PubMed ID
dgv3790n100 CNV gain 25217958
dgv694e199 CNV deletion 23128226
esv1427533 CNV deletion 17803354
esv1722218 CNV insertion 17803354
esv24650 CNV gain 19812545
esv2668900 CNV deletion 23128226
esv2719924 CNV deletion 23290073
esv2762493 CNV loss 21179565
esv3555066 CNV deletion 23714750
esv3590400 CNV loss 21293372
esv3590401 CNV loss 21293372
esv9230 CNV loss 19470904
nsv1114068 CNV deletion 24896259
nsv1134852 CNV deletion 24896259
nsv1153329 CNV deletion 26484159
nsv2682 CNV deletion 18451855
nsv428395 CNV gain 18775914
nsv525132 CNV loss 19592680
nsv581469 CNV loss 21841781
nsv819346 CNV gain 19587683
nsv820661 CNV deletion 20802225
nsv828920 CNV loss 20364138

Variation tolerance for VIT Gene

Residual Variation Intolerance Score: 58.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.38; 92.73% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VIT Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VIT

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VIT Gene

Disorders for VIT Gene

Relevant External Links for VIT

Genetic Association Database (GAD)
VIT
Human Genome Epidemiology (HuGE) Navigator
VIT
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VIT

No disorders were found for VIT Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VIT Gene

Publications for VIT Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 3 4 64
  5. Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere. (PMID: 12388743) Whittaker C.A. … Hynes R.O. (Mol. Biol. Cell 2002) 3 22 64

Products for VIT Gene

Sources for VIT Gene

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