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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VIM Gene

protein-coding   GIFtS: 73
GCID: GC10P017270

Vimentin

Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
vimentin1 2
CTRCT302

External Ids:    HGNC: 126921   Entrez Gene: 74312   Ensembl: ENSG000000260257   OMIM: 1930605   UniProtKB: P086703   

Export aliases for VIM gene to outside databases

Previous GC identifers: GC10P017253 GC10P017421 GC10P017275 GC10P017310


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 neurilemmoma, and glomangiosarcoma, and among its related super-pathways are Striated Muscle Contraction and Cytoskeleton remodeling Neurofilaments. GO annotations related to this gene include structural constituent of cytoskeleton and identical protein binding. An important paralog of this gene is LMNB1.

UniProtKB/Swiss-Prot: VIME_HUMAN, P08670
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
Function: Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2

Gene Wiki entry for VIM (Vimentin) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NT_008705.16  NC_018921.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VIM gene promoter:
         AREB6   Spz1   p53   MyoD   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): VIM promoter sequence
   Search SABiosciences Chromatin IP Primers for VIM

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VIM


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10p13   Ensembl cytogenetic band:  10p13   HGNC cytogenetic band: 10p13

VIM Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VIM gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P017270:  view genomic region     (about GC identifiers)

Start:
17,270,258 bp from pter      End:
17,279,592 bp from pter
Size:
9,335 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: VIME_HUMAN, P08670 (See protein sequence)
Recommended Name: Vimentin  
Size: 466 amino acids; 53652 Da
Subunit: 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) (By similarity). Interacts with SLC6A4. Interacts
with STK33. Interacts with LARP6. Interacts with RAB8B (By similarity)
Subcellular location: Cytoplasm
Sequence caution: Sequence=BAB71275.1; Type=Miscellaneous discrepancy; Note=Intron retention;
6/10 PDB 3D structures from and Proteopedia for VIM (see all 10):
1GK4 (3D)        1GK6 (3D)        1GK7 (3D)        3G1E (3D)        3KLT (3D)        3S4R (3D)    
Secondary accessions: B0YJC2 D3DRU4 Q15867 Q15868 Q15869 Q548L2 Q6LER9 Q8N850 Q96ML2 Q9NTM3

Explore the universe of human proteins at neXtProt for VIM: NX_P08670

Explore proteomics data for VIM at MOPED 

Post-translational modifications:

  • UniProtKB: 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
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P08670

  • VIM Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    VIM Protein Expression
    REFSEQ proteins: NP_003371.2  
    ENSEMBL proteins: 
     ENSP00000224237   ENSP00000435613   ENSP00000431702   ENSP00000391842   ENSP00000446007  
    Reactome Protein details: P08670
    Human Recombinant Protein Products for VIM: 
    Browse Purified and Recombinant Proteins at EMD Millipore
    R&D Systems Recombinant & Natural Proteins for VIM (Vimentin)
    Enzo Life Sciences proteins for VIM
    OriGene Purified Protein for VIM
    OriGene Protein Over-expression Lysate for VIM
    OriGene MassSpec for VIM 
    OriGene Custom Protein Services for VIM
    GenScript Custom Purified and Recombinant Proteins Services for VIM
    Novus Biologicals VIM Proteins
    Novus Biologicals VIM Lysates
    Sino Biological Recombinant Protein for VIM
    Sino Biological Cell Lysate for VIM 
    ProSpec Recombinant Protein for VIM
    Cloud-Clone Corp. Proteins for VIM 

    Gene Ontology (GO): 5/10 cellular component terms (GO ID links to tree view) (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA9150946
    GO:0005777peroxisome IDA17881773
    GO:0005829cytosol TAS--
    GO:0005856cytoskeleton TAS16130169
    GO:0005882intermediate filament IDA11889032

    VIM for ontologies           About GeneDecksing



    VIM Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of VIM
    R&D Systems Antibodies for VIM (Vimentin)
    Cell Signaling Technology (CST) Antibodies for VIM  (vimentin)
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    OriGene Custom Antibody Services for VIM
    GenScript Superior Antibodies for VIM
    Novus Biologicals VIM Antibodies
    Abcam antibodies for VIM
    Cloud-Clone Corp. Antibodies for VIM 
    ThermoFisher Antibody for VIM
    LSBio Antibodies in human, mouse, rat for VIM 

    Assay Products for VIM: 
    Browse Kits and Assays available from EMD Millipore
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    Browse R&D Systems for biochemical assays
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    Cell Signaling Technology (CST) Sandwich ELISA Kits for VIM (vimentin)
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for VIM 
    Cloud-Clone Corp. CLIAs for VIM


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    IFF3: Intermediate filaments type III

    4 InterPro protein domains:
     IPR006821 Intermed_filament_DNA-bd
     IPR018039 Intermediate_filament_CS
     IPR001664 IF
     IPR016044 F

    Graphical View of Domain Structure for InterPro Entry P08670

    ProtoNet protein and cluster: P08670

    1 Blocks protein domain: IPB001664 Intermediate filament protein

    UniProtKB/Swiss-Prot: VIME_HUMAN, P08670
    Domain: The central alpha-helical coiled-coil rod region mediates elementary homodimerization
    Similarity: Belongs to the intermediate filament family


    VIM for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VIME_HUMAN, P08670
    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
    Function: Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2

         Genatlas biochemistry entry for VIM:
    vimentin,intermediate filament protein,expressed in cells of mesenchymal origin,regulated by an antisilencer
    element

         Gene Ontology (GO): 5/7 molecular function terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005198structural molecule activity ----
    GO:0005200structural constituent of cytoskeleton IDA11889032
    GO:0005212structural constituent of eye lens IEA--
    GO:0005515protein binding IPI11827972
    GO:0008022protein C-terminus binding IPI19270731
         
    VIM for ontologies           About GeneDecksing


    Phenotypes:
         5 GenomeRNAi human phenotypes for VIM:
     Decreased Hepatitis C virus re  Decreased focal adhesion (FA)   Decreased viability with pacli  Increased gamma-H2AX phosphory 
     Weaker migration 

         13 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Vim):
     behavior/neurological  cardiovascular system  cellular  embryogenesis  growth/size 
     homeostasis/metabolism  immune system  mortality/aging  muscle  nervous system 
     reproductive system  respiratory system  vision/eye 

    VIM for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Vimtm2Cba for VIM

       inGenious Targeting Laboratory - Custom generated mouse model solutions for VIM 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for VIM

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for VIM 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for VIM 

    miRNA
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    miRTarBase miRNAs that target VIM:
    hsa-mir-17 (MIRT005028), hsa-mir-124 (MIRT004724)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat VIM
    8/17 QIAGEN miScript miRNA Assays for microRNAs that regulate VIM (see all 17):
    hsa-miR-320a hsa-miR-875-3p hsa-miR-509-5p hsa-miR-488 hsa-miR-548a-3p hsa-miR-124 hsa-miR-548x hsa-miR-506
    SwitchGear 3'UTR luciferase reporter plasmidVIM 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
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    Gene Editing
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    Sirion Biotech Customized adenovirus for overexpression of VIM

    Clone
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    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
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    OriGene ORF clones in mouse, rat for VIM
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: VIM (NM_003380)
    Sino Biological Human cDNA Clone for VIM
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for VIM
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VIM
    Sirion Biotech Customized lentivirus for stable overexpression of VIM 
                         Customized lentivirus expression plasmids for stable overexpression of VIM 

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    Search LifeMap BioReagents cell lines for VIM
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VIM


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for VIM About   (see all 17)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Striated Muscle Contraction
    Striated Muscle Contraction0.87
    Muscle contraction0.65
    Striated Muscle Contraction0.87
    2Cytoskeleton remodeling Neurofilaments
    Cytoskeleton remodeling Neurofilaments0.91
    Cytoplasmic microtubules0.32
    3Apoptotic cleavage of cellular proteins
    Apoptotic cleavage of cellular proteins0.73
    Caspase-mediated cleavage of cytoskeletal proteins0.32
    Apoptotic execution phase0.73
    4Rho Family GTPases
    Rho Family GTPases0.61
    ILK Signaling0.49
    5Cell adhesion Endothelial cell contacts by junctional mechanisms
    Cell adhesion Endothelial cell contacts by junctional mechanisms0.97

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    4 EMD Millipore Pathways for VIM
        Cytoskeleton remodeling Neurofilaments
    Cell adhesion Endothelial cell contacts by junctional mechanisms
    Cytoplasmic microtubules
    Cytoskeleton remodeling Keratin filaments

    4 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for VIM
        ILK Signaling
    Rho Family GTPases
    14-3-3 Induced Intracellular Signaling
    WNT Signaling

    1 Cell Signaling Technology (CST) Pathway for VIM
        Cytoskeletal Signaling

    3 GeneGo (Thomson Reuters) Pathways for VIM
        Cytoskeleton remodeling Keratin filaments
    Cell adhesion Endothelial cell contacts by junctional mechanisms
    Cytoskeleton remodeling Neurofilaments

    5/6 BioSystems Pathways for VIM (see all 6)
        Spinal Cord Injury
    Alpha6-Beta4 Integrin Signaling Pathway
    TCR Signaling Pathway
    Striated Muscle Contraction
    Aurora B signaling


    5/6        Reactome Pathways for VIM (see all 6)
        Apoptotic execution phase
    Muscle contraction
    Apoptotic cleavage of cellular proteins
    Caspase-mediated cleavage of cytoskeletal proteins
    Apoptosis


    2         Kegg Pathways  (Kegg details for VIM):
        Epstein-Barr virus infection
    MicroRNAs in cancer


    VIM for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for VIM

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/1117 Interacting proteins for VIM (P086701, 2, 3 ENSP000002242374) via UniProtKB, MINT, STRING, and/or I2D (see all 1117)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KAT7O952511, 2, 3, ENSP000002590214EBI-353844,EBI-473199 MINT-3980250 MINT-64943 MINT-66105 MINT-8277050 I2D: score=7 STRING: ENSP00000259021
    CRMP1Q141941, 2, 3, ENSP000003216064EBI-353844,EBI-473101 MINT-3980404 MINT-8277004 MINT-3981786 I2D: score=3 STRING: ENSP00000321606
    CHD3Q128732, 3, ENSP000003697164MINT-3979536 MINT-7945693 MINT-3980267 I2D: score=3 STRING: ENSP00000369716
    SIRT6Q8N6T72, 3, ENSP000003373324MINT-64930 MINT-8270737 I2D: score=4 STRING: ENSP00000337332
    YWHAZP631042, 3, ENSP000003095034MINT-3297793 MINT-7899812 I2D: score=4 STRING: ENSP00000309503
    About this table

    Gene Ontology (GO): 5/11 biological process terms (GO ID links to tree view) (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006915apoptotic process TAS--
    GO:0006921cellular component disassembly involved in execution phase of apoptosis TAS--
    GO:0006928cellular component movement TAS16130169
    GO:0010977negative regulation of neuron projection development IEA--
    GO:0014002astrocyte development IEA--

    VIM for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    VIM for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for VIM (VIME)

    1 HMDB Compound for VIM    About this table
    CompoundSynonyms CAS #PubMed Ids
    CarnosineBeta-Alanyl-L-histidine (see all 14)305-84-017522447

    10/156 Novoseek inferred chemical compound relationships for VIM gene (see all 156)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    b 723 71.5 37 7868083 (3), 12883236 (3), 12046609 (2), 1376598 (1) (see all 32)
    mucicarmine 71.4 8 16334025 (1), 11858401 (1), 10405240 (1), 8776426 (1) (see all 8)
    paraffin 67.4 66 1693875 (1), 1699393 (1), 2029088 (1), 7524376 (1) (see all 62)
    reticulin 63.7 13 7792953 (1), 11858401 (1), 16713546 (1), 8340101 (1) (see all 11)
    progesterone 62.7 184 19269675 (4), 12090595 (2), 15088145 (2), 11866908 (2) (see all 99)
    estrogen 58.4 180 19269675 (4), 12004356 (3), 15088145 (2), 2153347 (2) (see all 99)
    hematoxylin 56.5 24 7512798 (1), 15049161 (1), 10767834 (1), 16949932 (1) (see all 23)
    matrigel 53.1 9 7528440 (1), 19397698 (1), 11688960 (1), 1793731 (1) (see all 8)
    cp-49 47.7 8 7615661 (3), 7781747 (2), 10627819 (1), 17927688 (1) (see all 5)
    s 100 47.4 7 8878020 (2), 11253140 (1), 11253120 (1), 7706516 (1) (see all 6)

    Search CenterWatch for drugs/clinical trials and news about VIM / VIME

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for VIM gene: 
    NM_003380.3  

    Unigene Clusters for VIM:

    Vimentin
    Hs.455493  [show with all ESTs], Hs.691131  [show with all ESTs]
    Unigene Representative Sequences: NM_003380, BM458017
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000478317 ENST00000478746 ENST00000497849 ENST00000224237 ENST00000487938
    ENST00000485947 ENST00000469543 ENST00000421459 ENST00000495528 ENST00000544301(uc001iou.2)

    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    8/17 QIAGEN miScript miRNA Assays for microRNAs that regulate VIM (see all 17):
    hsa-miR-320a hsa-miR-875-3p hsa-miR-509-5p hsa-miR-488 hsa-miR-548a-3p hsa-miR-124 hsa-miR-548x hsa-miR-506
    SwitchGear 3'UTR luciferase reporter plasmidVIM 3' UTR sequence
    Inhib. RNA
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VIM
    Sirion Biotech Customized lentivirus for stable overexpression of VIM 
                         Customized lentivirus expression plasmids for stable overexpression of VIM 
    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat VIM
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat VIM

    Additional mRNA sequence: X16478.1 

    24/184 DOTS entries (see all 184):

    DT.100736301  DT.99925994  DT.91733250  DT.95153735  DT.100736262  DT.97861183  DT.102844050  DT.100736286 
    DT.100894798  DT.100736247  DT.100736347  DT.100736370  DT.92344625  DT.100736249  DT.99926544  DT.100736367 
    DT.85103186  DT.95153671  DT.121233616  DT.97854035  DT.121233524  DT.100736330  DT.92407751  DT.100736329 

    24/4539 AceView cDNA sequences (see all 4539):

    BE897061 AI669593 AI890944 AU118716 BQ961599 BQ948287 CN484557 BM705623 
    CA389385 BQ437657 AI680411 AW170808 BQ636773 BE386599 BU629032 BP341734 
    BF726251 CA420780 AU118425 CB126459 BQ952257 CD678423 BE891034 CA422203 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for VIM    About this scheme

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


    ECgene alternative splicing isoforms for VIM

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    VIM expression in normal human tissues (normalized intensities)      VIM embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCCAAATCGA
    VIM Expression
    About this image


    VIM expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/48 selected tissues (see all 48) fully expand
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 54 entries
             Multinuclear Myocytes Sacral Back Muscles
     
     Somite (Muscoskeletal System)    fully expand to see all 33 entries
             Myoblasts Thoracic Primary Hypaxial Myotome
             skeleton/axial skeleton   
     
     Brain (Nervous System)    fully expand to see all 27 entries
             Midbrain tegmentum
             Trigeminal Ganglion   
     
     Limb (Muscoskeletal System)    fully expand to see all 14 entries
             Multinuclear Myocytes Forelimb Dorsal Muscles
             limb/forelimb   
     
     Heart (Cardiovascular System)    fully expand to see all 7 entries
             Cardiac Fibroblasts Myocardium
             Cardiac stem cells
             heart/ventricle   

    See VIM Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VIM

    SOURCE GeneReport for Unigene clusters: Hs.455493 Hs.691131

    UniProtKB/Swiss-Prot: VIME_HUMAN, P08670
    Tissue specificity: Highly expressed in fibroblasts, some expression in T- and B-lymphocytes, and little or no
    expression in Burkitt's lymphoma cell lines. Expressed in many hormone-independent mammary carcinoma cell lines

        SABiosciences Expression via Pathway-Focused PCR Arrays including VIM (see all 8): 
              Nephrotoxicity in human mouse rat
              Oxidative Stress in human mouse rat
              Cell Motility in human mouse rat
              Cardiotoxicity in human mouse rat
              Mesenchymal Stem Cell in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for VIM gene from 5/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vim1 , 5 vimentin1, 5 91.7(n)1
    97.42(a)1
      2 (10.04 cM)5
    223521  NM_011701.41  NP_035831.21 
     135739275 
    chicken
    (Gallus gallus)
    Aves VIM1 vimentin 82.61(n)
    87.61(a)
      420519  NM_001048076.1  NP_001041541.1 
    lizard
    (Anolis carolinensis)
    Reptilia VIM6
    vimentin
    74(a)
    1 ↔ 1
    6(18296483-18332087)
    African clawed frog
    (Xenopus laevis)
    Amphibia vim12 vimentin 1 77.54(n)    BC045052.1 
    zebrafish
    (Danio rerio)
    Actinopterygii AF069994.12   -- 77.47(n)   140599  AF069994.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for VIM gene
    LMNB12  INA2  LMNA2  PRPH2  NEFM2  DES2  LMNB22  NEFH2  
    GFAP2  
    18/67 SIMAP similar genes for VIM using alignment to 4 protein entries:     VIME_HUMAN (see all proteins) (see all similar genes):
    DES    tmp_locus_29    PRPH    KRTHB6    GFAP    DKFZp761K0922
    NEFM    INA    NEFL    KRT4    KRTHB1    KRT1
    KRT5    keratin    KRT76    KRT79    KRT3    KRT6A

    VIM for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for VIM
    PGOHUM00000243352


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/275 SNPs in VIM are shown (see all 275)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1219177751,2
    Cpathogenic117180432(+) TCTACA/GAGGAG 2 K E mis10--------
    rs1144108201,2
    C,F--17179469(+) GCCCCG/AAGACC 1 -- int11Minor allele frequency- A:0.23WA 118
    rs37584121,2
    C,F,A--17179472(-) GGCGGT/CCTCGG 1 -- int111Minor allele frequency- C:0.38MN EA NS NA CSA WA 763
    rs1910830591,2
    --17179524(+) CCCCTC/TTGGTT 1 -- int10--------
    rs1446106561,2
    --17179551(+) CCCCCC/TTCACC 1 -- int10--------
    rs1837222521,2
    --17179605(+) AGACTA/GTCATC 1 -- int10--------
    rs37584111,2
    C,F,A,H--17179670(-) GGGGCC/GTGGGA 1 -- int16Minor allele frequency- G:0.17NS NA WA EA 570
    rs1891569901,2
    --17179752(+) GCTGGC/GGCGCT 1 -- int10--------
    rs1112940491,2
    C--17179835(+) TCCAGC/TCCTCT 1 -- ut510--------
    rs1928675291,2
    C--17179864(+) TCCCCA/GCGCCA 1 -- ut510--------

    HapMap Linkage Disequilibrium report for VIM (17270258 - 17279592 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for VIM:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2659900CNV Deletion23128226
    nsv508571CNV Loss20534489
    nsv831801CNV Gain17160897
    nsv894908CNV Gain21882294


    Human Gene Mutation Database (HGMD): VIM

    Locus Specific Mutation Databases (LSDB): VIM
    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 193060    OMIM disorders: --

    20/346 diseases for VIM (see all 346):    About MalaCards
    neurilemmoma    glomangiosarcoma    hydromyelia    prostate sarcoma
    balloon cell malignant melanoma    granular cell tumor    adenoiditis    mucinous cystadenocarcinoma
    adenomatoid tumor    biphasic synovial sarcoma    adenoid squamous cell carcinoma    astroblastoma
    osteoblastoma    ovarian mucinous cystadenocarcinoma    prostate leiomyoma    dermoid cyst of ovary
    radiation induced meningioma    clear cell meningioma    clear cell ependymoma    prostate stromal sarcoma

    3 diseases from the University of Copenhagen DISEASES database for VIM:
    Essential tremor     Parkinson's disease     Cancer

    VIM for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    10/94 Novoseek inferred disease relationships for VIM gene (see all 94)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tumors 86.2 1864 2153347 (5), 7518849 (5), 18632620 (4), 2173410 (4) (see all 99)
    rhabdoid tumor 83.6 9 15471430 (1), 19432675 (1), 11557780 (1), 8781656 (1) (see all 9)
    myoepithelioma 83.4 11 1694334 (1), 15619979 (1), 15717758 (1), 16099771 (1) (see all 10)
    carcinosarcoma 82 8 1696005 (1), 18281472 (1), 15132766 (1), 1283991 (1) (see all 8)
    sarcoma epithelioid 81 13 7679559 (3), 1689556 (1), 19997734 (1), 12946229 (1) (see all 9)
    sarcoma 80.1 45 1845482 (2), 7692876 (2), 1928559 (1), 1284388 (1) (see all 37)
    myofibroblastoma 78.7 4 10235504 (1), 9805854 (1), 1661895 (1), 1918406 (1)
    stromal tumors 78.3 11 7527534 (2), 16550975 (1), 12475434 (1), 14668550 (1) (see all 9)
    carcinoma spindle cell 76.9 6 9872659 (1), 8005741 (1), 2130227 (1), 15897741 (1)
    metastasis 76.7 87 18184460 (4), 20460738 (3), 18383865 (3), 15328185 (2) (see all 58)

    Genetic Association Database (GAD): VIM
    Human Genome Epidemiology (HuGE) Navigator: VIM (4 documents)

    Export disorders for VIM gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for VIM gene, integrated from 9 sources (see all 2970):
    (articles sorted by number of sources associating them with VIM)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The Serine/threonine kinase Stk33 exhibits autophosphorylation and phosphorylates the intermediate filament protein Vimentin. (PubMed id 18811945)1, 2, 9 Brauksiepe B....Schmidt E.R. (2008)
    2. The cellular distribution of serotonin transporter is impeded on serotonin-altered vimentin network. (PubMed id 19270731)1, 2, 9 Ahmed B.A....Kilic F. (2009)
    3. Specific in vivo phosphorylation sites determine the assembly dynamics of vimentin intermediate filaments. (PubMed id 14762106)1, 2, 9 Eriksson J.E.... Goldman R.D. (2004)
    4. SEREX identification of new tumour-associated antigens in cutaneous T-cell lymphoma. (PubMed id 14996095)1, 2, 9 Hartmann T.B.... Eichmueller S. (2004)
    5. Cdk5 mediates vimentin Ser56 phosphorylation during GTP-induced secretion by neutrophils. (PubMed id 21465480)1, 2 Lee K.Y.... Rosales J.L. (2012)
    6. A novel role of vimentin filaments: binding and stabilization of collagen mRNAs. (PubMed id 21746880)1, 2 Challa A.A. and Stefanovic B. (2011)
    7. Atomic structure of vimentin coil 2. (PubMed id 20176112)1, 2 Nicolet S....Strelkov S.V. (2010)
    8. Association study of 182 candidate genes in anorexia nervosa. (PubMed id 20468064)1, 4 Pinheiro A.P....Woodside D.B. (2010)
    9. Oxidative stress, telomere length and biomarkers of physical aging in a cohort aged 79 years from the 1932 Scottish Mental Survey. (PubMed id 18977241)1, 4 Starr J.M....Deary I.J. (2008)
    10. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. (PubMed id 17601350)1, 4 Harris S.E....Deary I.J. (2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 7431 HGNC: 12692 AceView: VIM Ensembl:ENSG00000026025 euGenes: HUgn7431
    ECgene: VIM Kegg: 7431 H-InvDB: VIM

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for VIM Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for VIM Genetics and Cytogenetics in Oncology and Haematology
    Wikipedia http://en.wikipedia.org/wiki/Vimentin

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for VIM gene:
    Search GeneIP for patents involving VIM

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

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