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Aliases for VIM Gene

Aliases for VIM Gene

  • Vimentin 2 3
  • CTRCT30 3 6
  • Epididymis Luminal Protein 113 3
  • HEL113 3

External Ids for VIM Gene

Summaries for VIM Gene

Entrez Gene Summary for VIM Gene

  • This gene encodes a member of the intermediate filament family. Intermediate filamentents, along with microtubules and actin microfilaments, make up the cytoskeleton. The protein encoded by this gene is responsible for maintaining cell shape, integrity of the cytoplasm, and stabilizing cytoskeletal interactions. It is also involved in the immune response, and controls the transport of low-density lipoprotein (LDL)-derived cholesterol from a lysosome to the site of esterification. It functions as an organizer of a number of critical proteins involved in attachment, migration, and cell signaling. Mutations in this gene causes a dominant, pulverulent cataract.[provided by RefSeq, Jun 2009]

GeneCards Summary for VIM Gene

VIM (Vimentin) is a Protein Coding gene. Diseases associated with VIM include balloon cell malignant melanoma and glomangiosarcoma. Among its related pathways are ERK Signaling and ERK Signaling. GO annotations related to this gene include identical protein binding and structural constituent of cytoskeleton. An important paralog of this gene is LMNB2.

UniProtKB/Swiss-Prot for VIM Gene

  • Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally.

  • Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.

Gene Wiki entry for VIM Gene

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

Genomics for VIM Gene

Genomic Location for VIM Gene

Start:
17,227,935 bp from pter
End:
17,237,593 bp from pter
Size:
9,659 bases
Orientation:
Plus strand

Genomic View for VIM Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VIM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VIM Gene

Regulatory Elements for VIM Gene

Proteins for VIM Gene

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

    Protein Symbol:
    P08670-VIME_HUMAN
    Recommended name:
    Vimentin
    Protein Accession:
    P08670
    Secondary Accessions:
    • B0YJC2
    • D3DRU4
    • Q15867
    • Q15868
    • Q15869
    • Q548L2
    • Q6LER9
    • Q8N850
    • Q96ML2
    • Q9NTM3

    Protein attributes for VIM Gene

    Size:
    466 amino acids
    Molecular mass:
    53652 Da
    Quaternary structure:
    • Homopolymer assembled from elementary dimers. Interacts with HCV core protein. Interacts with LGSN and SYNM. Interacts (via rod region) with PLEC (via CH 1 domain). Interacts with SLC6A4. Interacts with STK33. Interacts with LARP6. Interacts with RAB8B. Interacts with TOR1A; the interaction associates TOR1A with the cytoskeleton. Interacts with TOR1AIP1. Interacts with BCAS3.
    SequenceCaution:
    • Sequence=BAB71275.1; Type=Miscellaneous discrepancy; Note=Product of a cloning artifact.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for VIM Gene

neXtProt entry for VIM Gene

Proteomics data for VIM Gene at MOPED

Post-translational modifications for VIM Gene

  • Filament disassembly during mitosis is promoted by phosphorylation at Ser-55 as well as by nestin (By similarity). One of the most prominent phosphoproteins in various cells of mesenchymal origin. Phosphorylation is enhanced during cell division, at which time vimentin filaments are significantly reorganized. Phosphorylation by PKN1 inhibits the formation of filaments. Phosphorylated at Ser-56 by CDK5 during neutrophil secretion in the cytoplasm. Phosphorylated by STK33.
  • O-glycosylated during cytokinesis at sites identical or close to phosphorylation sites, this interferes with the phosphorylation status.
  • S-nitrosylation is induced by interferon-gamma and oxidatively-modified low-densitity lipoprotein (LDL(ox)) possibly implicating the iNOS-S100A8/9 transnitrosylase complex.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys97, Lys104, Lys120, Lys129, Lys139, Lys143, Lys168, Lys188, Lys223, Lys236, Lys282, Lys292, Lys294, Lys313, Lys334, Lys373, Lys402, Lys439, and Lys445
  • Glycosylation at Ser7, Thr33, and Ser34

Other Protein References for VIM Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for VIM Gene

Domains for VIM Gene

Gene Families for VIM Gene

HGNC:
  • IFF2 :Intermediate filaments type II, keratins (basic)

Protein Domains for VIM Gene

UniProtKB/Swiss-Prot:

VIME_HUMAN
Domain:
  • The central alpha-helical coiled-coil rod region mediates elementary homodimerization:
    • P08670
  • The [IL]-x-C-x-x-[DE] motif is a proposed target motif for cysteine S-nitrosylation mediated by the iNOS-S100A8/A9 transnitrosylase complex.:
    • P08670
Family:
  • Belongs to the intermediate filament family.:
    • P08670
genes like me logo Genes that share domains with VIM: view

Function for VIM Gene

Molecular function for VIM Gene

GENATLAS Biochemistry: vimentin,intermediate filament protein,expressed in cells of mesenchymal origin,regulated by an antisilencer element
UniProtKB/Swiss-Prot Function: Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally.
UniProtKB/Swiss-Prot Function: Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.

Gene Ontology (GO) - Molecular Function for VIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001948 glycoprotein binding IPI 19420356
GO:0003725 double-stranded RNA binding IDA 21266579
GO:0005198 structural molecule activity --
GO:0005200 structural constituent of cytoskeleton IDA 11889032
GO:0005212 structural constituent of eye lens IEA --
genes like me logo Genes that share ontologies with VIM: view
genes like me logo Genes that share phenotypes with VIM: view

Animal Models for VIM Gene

MGI Knock Outs for VIM:

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for VIM Gene

Localization for VIM Gene

Subcellular locations from UniProtKB/Swiss-Prot for VIM Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VIM Gene COMPARTMENTS Subcellular localization image for VIM gene
Compartment Confidence
cytoskeleton 5
cytosol 5
extracellular 5
peroxisome 5
mitochondrion 3
nucleus 2

Gene Ontology (GO) - Cellular Components for VIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 15846844
GO:0005777 peroxisome IDA 17881773
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton TAS 16130169
GO:0005882 intermediate filament IDA 11889032
genes like me logo Genes that share ontologies with VIM: view

Pathways for VIM Gene

genes like me logo Genes that share pathways with VIM: view

Gene Ontology (GO) - Biological Process for VIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006915 apoptotic process TAS --
GO:0006921 cellular component disassembly involved in execution phase of apoptosis TAS --
GO:0006928 movement of cell or subcellular component TAS 16130169
GO:0010628 positive regulation of gene expression IEA --
GO:0010977 negative regulation of neuron projection development IEA --
genes like me logo Genes that share ontologies with VIM: view

Compounds for VIM Gene

(1) HMDB Compounds for VIM Gene

Compound Synonyms Cas Number PubMed IDs
Carnosine
  • Beta-Alanyl-L-histidine
305-84-0

(156) Novoseek inferred chemical compound relationships for VIM Gene

Compound -log(P) Hits PubMed IDs
b 723 71.5 37
mucicarmine 71.4 8
paraffin 67.4 62
reticulin 63.7 11
progesterone 62.7 109
genes like me logo Genes that share compounds with VIM: view

Transcripts for VIM Gene

Unigene Clusters for VIM Gene

Vimentin:
Representative Sequences:

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

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11
SP1: - - -
SP2:
SP3:
SP4: - -
SP5:

Relevant External Links for VIM Gene

GeneLoc Exon Structure for
VIM
ECgene alternative splicing isoforms for
VIM

Expression for VIM Gene

mRNA expression in normal human tissues for VIM Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Artery - Aorta (4.3) and Artery - Tibial (4.2).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for VIM Gene

SOURCE GeneReport for Unigene cluster for VIM Gene Hs.455493

mRNA Expression by UniProt/SwissProt for VIM Gene

P08670-VIME_HUMAN
Tissue specificity: Highly expressed in fibroblasts, some expression in T- and B-lymphocytes, and little or no expression in Burkitts lymphoma cell lines. Expressed in many hormone-independent mammary carcinoma cell lines.
genes like me logo Genes that share expressions with VIM: view

Orthologs for VIM Gene

This gene was present in the common ancestor of chordates.

Orthologs for VIM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VIM 36
  • 99.43 (n)
  • 99.57 (a)
VIM 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VIM 36
  • 92.64 (n)
  • 97.57 (a)
VIM 37
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VIM 36
  • 94.49 (n)
  • 98.07 (a)
VIM 37
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vim 36
  • 91.61 (n)
  • 97.35 (a)
Vim 16
Vim 37
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VIM 37
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VIM 37
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vim 36
  • 91.61 (n)
  • 97.35 (a)
chicken
(Gallus gallus)
Aves VIM 36
  • 83.59 (n)
  • 88.37 (a)
VIMENTIN 37
  • 89 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VIM 37
  • 75 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia vim1 36
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.11198 36
vim 36
  • 73.45 (n)
  • 79.42 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11950 36
zebrafish
(Danio rerio)
Actinopterygii -- 36
vim 36
  • 71.83 (n)
  • 73.12 (a)
vim 37
  • 71 (a)
OneToMany
viml 37
  • 68 (a)
OneToMany
Species with no ortholog for VIM:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 VIM Gene

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

Paralogs for VIM Gene

Paralogs for VIM Gene

Pseudogenes.org Pseudogenes for VIM Gene

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

Variants for VIM Gene

Sequence variations from dbSNP and Humsavar for VIM Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type MAF
rs3249 -- 17,237,518(-) TTAAT(A/G)GTATT utr-variant-3-prime
rs4903 -- 17,233,862(+) CGTGA(C/T)GTACG reference, synonymous-codon
rs9059 -- 17,237,413(+) TAGTT(C/G/T)TTAAC utr-variant-3-prime
rs9235 -- 17,237,400(+) TAGGA(A/G)TAAGC utr-variant-3-prime
rs9484 -- 17,237,466(+) ATCTA(G/T)TTTAC utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
nsv894908 CNV Gain 21882294
nsv831801 CNV Gain 17160897
nsv508571 CNV Loss 20534489
esv2659900 CNV Deletion 23128226

Relevant External Links for VIM Gene

HapMap Linkage Disequilibrium report
VIM
Human Gene Mutation Database (HGMD)
VIM
Locus Specific Mutation Databases (LSDB)
VIM

Disorders for VIM Gene

(1) OMIM Diseases for VIM Gene (193060)

UniProtKB/Swiss-Prot

VIME_HUMAN
  • Cataract 30 (CTRCT30) [MIM:116300]: An opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for VIM Gene

(94) Novoseek inferred disease relationships for VIM Gene

Disease -log(P) Hits PubMed IDs
tumors 86.2 218
rhabdoid tumor 83.6 9
myoepithelioma 83.4 10
carcinosarcoma 82 8
sarcoma epithelioid 81 11

Relevant External Links for VIM

Genetic Association Database (GAD)
VIM
Human Genome Epidemiology (HuGE) Navigator
VIM
genes like me logo Genes that share disorders with VIM: view

Publications for VIM Gene

  1. SEREX identification of new tumour-associated antigens in cutaneous T-cell lymphoma. (PMID: 14996095) Hartmann T.B. … Eichmueller S. (Br. J. Dermatol. 2004) 3 4 23
  2. The serine/threonine kinase Stk33 exhibits autophosphorylation and phosphorylates the intermediate filament protein Vimentin. (PMID: 18811945) Brauksiepe B. … Schmidt E.R. (BMC Biochem. 2008) 3 4 23
  3. Specific in vivo phosphorylation sites determine the assembly dynamics of vimentin intermediate filaments. (PMID: 14762106) Eriksson J.E. … Goldman R.D. (J. Cell Sci. 2004) 3 4 23
  4. The cellular distribution of serotonin transporter is impeded on serotonin-altered vimentin network. (PMID: 19270731) Ahmed B.A. … Kilic F. (PLoS ONE 2009) 3 4 23
  5. Phosphorylation and reorganization of vimentin by p21-activated kinase (PAK). (PMID: 11895474) Goto H. … Inagaki M. (Genes Cells 2002) 3 23

Products for VIM Gene

  • Addgene plasmids for VIM

Sources for VIM Gene

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