Free for academic non-profit institutions. Other users need a Commercial license

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. Diseases associated with VIT include Syndromic X-Linked Intellectual Disability Snyder Type and Syndromic X-Linked Intellectual Disability. Gene Ontology (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.

Additional gene information for VIT Gene

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

Genomics for VIT Gene

GeneHancer (GH) Regulatory Elements for VIT Gene

Promoters and enhancers for VIT Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I036695 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 550.8 +0.3 292 2.4 CTCF ZNF449 GFI1B ZSCAN4 CEBPB RAD21 ZNF843 GATA3 PRDM6 SMC3 VIT GC02P036731
GH02I036703 Promoter 0.5 EPDnew 550.4 +6.9 6896 0.1 VIT GC02P036731
GH02I036753 Enhancer 0.7 ENCODE 7.7 +57.4 57373 1.5 SOX13 FOXA2 ZNF644 RARA NR2F6 CREM HOMEZ GATAD2A SOX5 NFIA VIT GC02P036764 GC02P036731
GH02I036657 Enhancer 0.9 ENCODE 4.5 -37.4 -37392 3.2 FOXA2 MLX ARID4B ETS1 SLC30A9 ATF7 FOS RUNX3 JUNB MXD4 CRIM1 VIT LOC100422559
GH02I036481 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 1.7 -208.9 -208924 11.8 FOXA2 SIN3A DMAP1 ETS1 FOS DEK RXRA NFYC REST PPARG CRIM1 FEZ2 VIT ENSG00000273090 GC02P036388
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VIT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VIT gene promoter:

Genomic Locations for VIT Gene

Genomic Locations for VIT Gene
chr2:36,696,690-36,814,794
(GRCh38/hg38)
Size:
118,105 bases
Orientation:
Plus strand
chr2:36,923,833-37,041,937
(GRCh37/hg19)

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 isoforms=2, 4, 5390 and isoforms=2, 4, 5520

No data available for DME Specific Peptides for VIT Gene

Domains & Families for VIT Gene

Gene Families for VIT Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for VIT Gene

Suggested Antigen Peptide Sequences for VIT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for VIT Gene

Function for VIT Gene

Molecular function for VIT Gene

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

Phenotypes From GWAS Catalog for VIT Gene

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 Models for VIT Gene

MGI Knock Outs for VIT:

Animal Model Products

CRISPR Products

miRNA for VIT Gene

miRTarBase miRNAs that target VIT

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VIT gene
Compartment Confidence
extracellular 4
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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VIT Gene

Pathways & Interactions 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

Drugs & Compounds for VIT Gene

No Compound Related Data Available

Transcripts for VIT Gene

Unigene Clusters for VIT Gene

Vitrin:
Representative Sequences:

CRISPR Products

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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

Evidence on tissue expression from TISSUES for VIT Gene

  • Nervous system(4.3)
  • Muscle(4.1)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with VIT: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VIT 33 34
  • 87.83 (n)
cow
(Bos Taurus)
Mammalia VIT 33 34
  • 85.84 (n)
mouse
(Mus musculus)
Mammalia Vit 33 16 34
  • 85.18 (n)
rat
(Rattus norvegicus)
Mammalia Vit 33
  • 84.39 (n)
oppossum
(Monodelphis domestica)
Mammalia VIT 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VIT 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves VIT 33 34
  • 71.14 (n)
lizard
(Anolis carolinensis)
Reptilia VIT 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100489513 33
  • 66.07 (n)
zebrafish
(Danio rerio)
Actinopterygii ch1073-291c23.1 34 33
  • 64.17 (n)
OneToOne
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 Variation AA Info Type
rs386352378 uncertain-significance, not provided 36,787,249(+) G/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000046152 -- 36,743,382(+) T/A genic_upstream_transcript_variant, intron_variant
rs1000058029 -- 36,810,107(+) C/A genic_downstream_transcript_variant, intron_variant
rs1000064014 -- 36,777,352(+) T/C genic_downstream_transcript_variant, intron_variant
rs1000076644 -- 36,798,743(+) A/G genic_downstream_transcript_variant, intron_variant

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

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

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)

Additional Variant Information 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

MalaCards: The human disease database

(3) MalaCards diseases for VIT Gene - From: DISEASES

Disorder Aliases PubMed IDs
syndromic x-linked intellectual disability snyder type
  • mental retardation, x-linked, snyder-robinson type
syndromic x-linked intellectual disability
  • syndromic intellectual disability, x-linked
hypersensitivity reaction disease
- elite association - COSMIC cancer census association via MalaCards
Search VIT in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VIT

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VIT: view

No data available for 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 JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  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 HF … Gray A (Genome research 2003) 3 4 58
  5. Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere. (PMID: 12388743) Whittaker CA … Hynes RO (Molecular biology of the cell 2002) 3 22 58

Products for VIT Gene

Sources for VIT Gene

Content
Loading form....