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Aliases for VIM Gene

Aliases for VIM Gene

External Ids for VIM Gene

Previous GeneCards Identifiers for VIM Gene

  • GC10P017253
  • GC10P017421
  • GC10P017275
  • GC10P017310
  • GC10P017270

Summaries for VIM Gene

Entrez Gene Summary for VIM Gene

  • This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients. [provided by RefSeq, Aug 2017]

GeneCards Summary for VIM Gene

VIM (Vimentin) is a Protein Coding gene. Diseases associated with VIM include Cataract 30, Multiple Types and Cataract 30. Among its related pathways are ERK Signaling and Cytoskeletal Signaling. Gene Ontology (GO) annotations related to this gene include identical protein binding and protein C-terminus binding. An important paralog of this gene is DES.

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

Additional gene information for VIM Gene

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

Genomics for VIM Gene

GeneHancer (GH) Regulatory Elements for VIM Gene

Promoters and enhancers for VIM 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
GH10J017226 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +3.6 3602 10.6 FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 ZFP41 MEF2D ZNF610 VIM-AS1 TRDMT1 VIM LOC105376438 LOC102724039 ENSG00000273153 ENSG00000234961
GH10J017212 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 28.7 -12.0 -11950 7.7 PKNOX1 FOXA2 ARNT IRF4 ZNF766 FOS SP3 JUNB ZNF592 SMARCA4 TRDMT1 VIM CUBN VIM-AS1
GH10J017021 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.8 -201.8 -201846 9.6 PKNOX1 ATF1 ARNT IRF4 NCOA2 TCF12 CBX5 GATA2 E2F8 FOS VIM CUBN ENSG00000234961 TRDMT1 GC10P016843
GH10J016999 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20 -222.7 -222686 11.8 PKNOX1 ATF1 ARNT ZNF133 FEZF1 NCOA2 TCF12 ZNF766 GATA2 ZNF548 VIM LOC105376438 ENSG00000234961 CUBN RSU1 TRDMT1 ST8SIA6 GC10P016843
GH10J017073 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 18.1 -151.8 -151814 4.8 L3MBTL2 JUN TAL1 CEBPB CBFA2T3 CEBPG EP300 SP1 JUND POLR2A VIM CUBN TRDMT1 GC10P016843
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VIM on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VIM gene promoter:
  • p53
  • MyoD
  • AREB6
  • Spz1

Genomic Locations for VIM Gene

Genomic Locations for VIM Gene
chr10:17,227,935-17,237,593
(GRCh38/hg38)
Size:
9,659 bases
Orientation:
Plus strand
chr10:17,270,258-17,279,592
(GRCh37/hg19)
Size:
9,335 bases
Orientation:
Plus strand

Genomic View for VIM Gene

Genes around VIM on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence 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 (PubMed:15846844). Interacts with LGSN and SYNM. Interacts (via rod region) with PLEC (via CH 1 domain) (By similarity). Interacts with SLC6A4 (PubMed:19270731). Interacts with STK33 (PubMed:18811945). Interacts with LARP6 (PubMed:21746880). Interacts with RAB8B (By similarity). Interacts with TOR1A; the interaction associates TOR1A with the cytoskeleton (PubMed:16361107, PubMed:18827015). Interacts with TOR1AIP1 (PubMed:16361107). Interacts with BCAS3 (PubMed:17505058). Interacts with DIAPH1 (PubMed:23325789). Identified in complexes that contain VIM, EZR, AHNAK, BFSP1, BFSP2, ANK2, PLEC, PRX and spectrin (By similarity). Interacts with EPPK1; interaction is dependent of higher-order structure of intermediate filament (PubMed:16923132). Interacts with the non-receptor tyrosine kinase SRMS; the interaction leads to phosphorylation of VIM (PubMed:29496907).
    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

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 (PubMed:21465480). Phosphorylated by STK33 (PubMed:18811945). Phosphorylated on tyrosine residues by SRMS (PubMed:29496907).
  • 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.
  • Ubiquitination at posLast=445445, posLast=373373, isoforms=313, posLast=294294, isoforms=282, isoforms=236, isoforms=188, isoforms=168, posLast=139139, posLast=129129, isoforms=120, and isoforms=97
  • Glycosylation at posLast=3434, posLast=3333, and isoforms=7
  • Modification sites at PhosphoSitePlus

Other Protein References for VIM Gene

Antibody Products

No data available for DME Specific Peptides for VIM Gene

Domains & Families for VIM Gene

Gene Families for VIM Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for VIM Gene

Suggested Antigen Peptide Sequences for VIM Gene

Graphical View of Domain Structure for InterPro Entry

P08670

UniProtKB/Swiss-Prot:

VIME_HUMAN :
  • The central alpha-helical coiled-coil IF rod domain mediates elementary homodimerization.
  • Belongs to the intermediate filament family.
Domain:
  • The central alpha-helical coiled-coil IF rod domain mediates elementary homodimerization.
  • 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.
Family:
  • Belongs to the intermediate filament family.
genes like me logo Genes that share domains with VIM: view

Function for VIM Gene

Molecular function for VIM Gene

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.
GENATLAS Biochemistry:
vimentin,intermediate filament protein,expressed in cells of mesenchymal origin,regulated by an antisilencer element

Phenotypes From GWAS Catalog for VIM Gene

Gene Ontology (GO) - Molecular Function for VIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003725 double-stranded RNA binding IDA 21266579
GO:0005198 structural molecule activity IEA --
GO:0005200 structural constituent of cytoskeleton IDA 11889032
GO:0005212 structural constituent of eye lens IEA --
GO:0005515 protein binding IPI 10852826
genes like me logo Genes that share ontologies with VIM: view
genes like me logo Genes that share phenotypes with VIM: view

Human Phenotype Ontology for VIM Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VIM Gene

MGI Knock Outs for VIM:
  • Vim Vim<tm1Cba>
  • Vim Vim<tm2Cba>

Animal Model Products

Clone Products

  • Addgene plasmids for VIM

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

Localization for VIM Gene

Subcellular locations from UniProtKB/Swiss-Prot for VIM Gene

Cytoplasm. Cytoplasm, cytoskeleton. Nucleus 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 VIM gene
Compartment Confidence
extracellular 5
cytoskeleton 5
peroxisome 5
cytosol 5
mitochondrion 3
nucleus 3
plasma membrane 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Intermediate filaments (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 9150946
GO:0005777 peroxisome IDA 17881773
GO:0005829 cytosol TAS --
GO:0005844 polysome IDA 20603131
GO:0005856 cytoskeleton TAS,IDA 16130169
genes like me logo Genes that share ontologies with VIM: view

Pathways & Interactions for VIM Gene

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

SIGNOR curated interactions for VIM Gene

Is activated by:
Is inactivated by:
Other effect:

Gene Ontology (GO) - Biological Process for VIM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010628 positive regulation of gene expression IEA --
GO:0010977 negative regulation of neuron projection development IEA --
GO:0014002 astrocyte development IEA --
GO:0016032 viral process IEA --
GO:0019221 cytokine-mediated signaling pathway TAS --
genes like me logo Genes that share ontologies with VIM: view

Drugs & Compounds for VIM Gene

(89) Drugs for VIM Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Dihydroartemisinin Approved, Investigational Pharma Target, ligand 100
Carnosine Investigational Pharma 0
Phenethyl isothiocyanate Investigational Pharma Target 12

(69) Additional Compounds for VIM Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with VIM: view

Transcripts for VIM Gene

mRNA/cDNA for VIM Gene

Unigene Clusters for VIM Gene

Vimentin:
Representative Sequences:

Clone Products

  • Addgene plasmids for VIM

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for VIM Gene

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

This gene is overexpressed in Artery - Aorta (x4.3) and Artery - Tibial (x4.2).

Protein differential expression in normal tissues from HIPED for VIM Gene

This gene is overexpressed in Bone marrow stromal cell (17.5) and Adipocyte (9.5).

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



Protein tissue co-expression partners for VIM Gene

NURSA nuclear receptor signaling pathways regulating expression of VIM Gene:

VIM

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.

Evidence on tissue expression from TISSUES for VIM Gene

  • Blood(5)
  • Liver(5)
  • Lung(5)
  • Skin(5)
  • Nervous system(5)
  • Eye(4.9)
  • Intestine(4.9)
  • Kidney(4.9)
  • Stomach(4.9)
  • Bone(4.8)
  • Heart(4.8)
  • Pancreas(4.7)
  • Spleen(4.7)
  • Thyroid gland(4.6)
  • Muscle(3.9)
  • Bone marrow(3.3)
  • Lymph node(3.1)
  • Adrenal gland(2.8)
  • Gall bladder(2.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VIM Gene

Germ Layers:
  • ectoderm
Systems:
  • nervous
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
General:
  • peripheral nervous system
genes like me logo Genes that share expression patterns 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 34 33
  • 99.43 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VIM 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VIM 34 33
  • 94.49 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VIM 34 33
  • 92.64 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vim 16 34 33
  • 91.61 (n)
rat
(Rattus norvegicus)
Mammalia Vim 33
  • 91.61 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VIM 34
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves VIMENTIN 34
  • 89 (a)
OneToOne
VIM 33
  • 83.59 (n)
lizard
(Anolis carolinensis)
Reptilia VIM 34
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vim 33
  • 73.45 (n)
Str.11198 33
African clawed frog
(Xenopus laevis)
Amphibia vim1 33
zebrafish
(Danio rerio)
Actinopterygii vim 34 33
  • 71.83 (n)
OneToMany
viml 34
  • 68 (a)
OneToMany
-- 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11950 33
Species where no ortholog for VIM was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for VIM: view image

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 Variation AA Info Type
rs1085307141 pathogenic, Cataract 30 17,230,709(+) A/G coding_sequence_variant, missense_variant
rs121917775 pathogenic, not-provided, Cataract 30, not provided, Cataract 30, multiple types (CTRCT30) [MIM:116300] 17,229,873(+) G/A coding_sequence_variant, missense_variant
rs4903 benign, Cataract 30 17,233,862(+) C/T coding_sequence_variant, synonymous_variant
rs79719081 benign, Cataract 30 17,235,159(+) C/T intron_variant
rs864309690 likely-pathogenic, pathogenic, Congenital cataract, Cataract 30 17,229,436(+) CC/C coding_sequence_variant, frameshift

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

Variant ID Type Subtype PubMed ID
dgv179e212 CNV loss 25503493
esv2659900 CNV deletion 23128226
nsv1039697 CNV loss 25217958
nsv508571 CNV deletion 20534489
nsv831801 CNV gain 17160897

Variation tolerance for VIM Gene

Residual Variation Intolerance Score: 15.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.85; 17.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VIM Gene

Human Gene Mutation Database (HGMD)
VIM
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VIM

SNP Genotyping and Copy Number Assay Products

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

Disorders for VIM Gene

MalaCards: The human disease database

(157) MalaCards diseases for VIM Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cataract 30, multiple types
  • ctrct30
cataract 30
  • ctrct30
malignant mixed mullerian tumor
  • carcinosarcoma
spindle cell carcinoma
  • sarcomatoid carcinoma
glomus tumor
  • glomus neoplasm
- elite association - COSMIC cancer census association via MalaCards
Search VIM in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VIME_HUMAN
  • Cataract 30, multiple types (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. {ECO:0000269 PubMed:19126778, ECO:0000269 PubMed:26694549, ECO:0000269 PubMed:28450710}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for VIM

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 VIM: view

No data available for Genatlas for VIM Gene

Publications for VIM Gene

  1. The cellular distribution of serotonin transporter is impeded on serotonin-altered vimentin network. (PMID: 19270731) Ahmed BA … Kilic F (PloS one 2009) 3 4 22 58
  2. The Serine/threonine kinase Stk33 exhibits autophosphorylation and phosphorylates the intermediate filament protein Vimentin. (PMID: 18811945) Brauksiepe B … Schmidt ER (BMC biochemistry 2008) 3 4 22 58
  3. SEREX identification of new tumour-associated antigens in cutaneous T-cell lymphoma. (PMID: 14996095) Hartmann TB … Eichmüller S (The British journal of dermatology 2004) 3 4 22 58
  4. Specific in vivo phosphorylation sites determine the assembly dynamics of vimentin intermediate filaments. (PMID: 14762106) Eriksson JE … Goldman RD (Journal of cell science 2004) 3 4 22 58
  5. Phosphoproteomics Analysis Identifies Novel Candidate Substrates of the Nonreceptor Tyrosine Kinase, Src-related Kinase Lacking C-terminal Regulatory Tyrosine and N-terminal Myristoylation Sites (SRMS). (PMID: 29496907) Goel RK … Lukong KE (Molecular & cellular proteomics : MCP 2018) 3 4 58

Products for VIM Gene

  • Addgene plasmids for VIM

Sources for VIM Gene