Human Gene VIM (uc001iou.2) Description and Page Index
  Description: Homo sapiens vimentin (VIM), mRNA.
RefSeq Summary (NM_003380): 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]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC066956.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2144120, SAMEA2148093 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000544301.7/ ENSP00000446007.1 RefSeq Select criteria :: based on conservation, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr10:17,270,258-17,279,592 Size: 9,335 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr10:17,271,422-17,279,270 Size: 7,849 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:17,270,258-17,279,592)mRNA (may differ from genome)Protein (466 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: VIME_HUMAN
DESCRIPTION: RecName: Full=Vimentin;
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.
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).
INTERACTION: Self; NbExp=5; IntAct=EBI-353844, EBI-353844; P31749:AKT1; NbExp=29; IntAct=EBI-353844, EBI-296087; P31751:AKT2; NbExp=6; IntAct=EBI-353844, EBI-296058; Q9H6U6:BCAS3; NbExp=3; IntAct=EBI-353844, EBI-6083685; Q14194:CRMP1; NbExp=2; IntAct=EBI-353844, EBI-473101; O95251:KAT7; NbExp=3; IntAct=EBI-353844, EBI-473199; O95361:TRIM16; NbExp=3; IntAct=EBI-353844, EBI-727384;
SUBCELLULAR LOCATION: Cytoplasm.
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.
DOMAIN: The central alpha-helical coiled-coil rod region mediates elementary homodimerization.
PTM: 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.
SIMILARITY: Belongs to the intermediate filament family.
SEQUENCE CAUTION: Sequence=BAB71275.1; Type=Miscellaneous discrepancy; Note=Intron retention;
WEB RESOURCE: Name=Wikipedia; Note=Vimentin entry; URL="http://en.wikipedia.org/wiki/Vimentin";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): VIM
CDC HuGE Published Literature: VIM
Positive Disease Associations: Forced Expiratory Volume , Forced Vital Capacity
Related Studies:
  1. Forced Expiratory Volume
    , , . [PubMed 0]
  2. Forced Vital Capacity
    , , . [PubMed 0]
  3. Forced Vital Capacity
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: VIM
Diseases sorted by gene-association score: cataract 30, pulverulent* (1666), malignant mixed mullerian tumor (37), spindle cell carcinoma (32), glomus tumor (31), clear cell ependymoma (30), spindle cell sarcoma (27), epithelioid sarcoma (23), chondroid chordoma (23), nodular hidradenoma (23), adenoid squamous cell carcinoma (22), granular cell tumor (20), malignant peripheral nerve sheath tumor (19), epithelioid leiomyosarcoma (19), adenomatoid tumor (19), intravascular papillary endothelial hyperplasia (18), chordoma (18), papillary tumor of the pineal region (18), infantile digital fibromatosis (18), odontogenic myxoma (18), malignant peritoneal mesothelioma (18), tubulocystic renal cell carcinoma (18), dendritic cell tumor (18), congenital epulis (18), reticulum cell sarcoma (18), central nervous system sarcoma (18), epulis (18), fibroma (18), angiolipoma (18), secretory meningioma (17), phyllode tumor (17), pleomorphic adenoma (16), rhabdoid meningioma (15), eccrine porocarcinoma (15), sternum cancer (15), ependymoblastoma (15), smooth muscle tumor (15), sertoli cell tumor (15), undifferentiated pleomorphic sarcoma (14), granulosa cell tumor of the ovary (13), giant axonal neuropathy (13), multicentric reticulohistiocytosis (13), endocervical adenocarcinoma (13), spindle cell lipoma (13), mesenchymal chondrosarcoma (13), senile angioma (13), regional odontodysplasia (13), giant cell tumor (12), glomangiomyoma (12), lymphangiectasis (12), embryonal sarcoma (12), liver angiosarcoma (12), papillary adenoma (12), perineurioma (12), angiosarcoma (12), myoepithelial carcinoma (11), dermatofibrosarcoma protuberans (11), melanotic neuroectodermal tumor (11), polymorphous low-grade adenocarcinoma (10), alveolar soft-part sarcoma (10), ovarian mucinous cystadenocarcinoma (10), granuloma annulare (10), hydromyelia (10), pericardial mesothelioma (10), gynandroblastoma (10), mast-cell sarcoma (10), hemangiopericytoma, malignant (10), cavernous hemangioma (10), fibromatosis (10), hidradenoma (9), ependymoma (9), parachordoma (9), chandler syndrome (9), esophagus squamous cell carcinoma (9), leiomyosarcoma (9), pleomorphic liposarcoma (9), endometrial mucinous adenocarcinoma (9), myoclonic cerebellar dyssynergia (9), anaplastic ependymoma (9), glomangioma (9), fibrous meningioma (9), cutaneous leiomyosarcoma (9), ameloblastic carcinoma (9), metanephric adenoma (9), fibrous histiocytoma (9), cystadenocarcinoma (9), meninges hemangiopericytoma (9), desmoplastic small round cell tumor (8), medulloepithelioma (8), liposarcoma (8), ossifying fibromyxoid tumor (8), primitive neuroectodermal tumor of the cervix uteri (8), chordoid meningioma (8), nodular lymphocyte predominant hodgkin lymphoma (8), syringoma (8), juvenile xanthogranuloma (8), cerebral primitive neuroectodermal tumor (8), monophasic synovial sarcoma (8), neuronal migration disorders (8), benign metastasizing leiomyoma (8), biphasic synovial sarcoma (8), primary hepatic neuroendocrine carcinoma (8), bednar tumor (8), lymphangiomatosis (8), congenital fibrosarcoma (8), gingival hypertrophy (8), endometrial stromal sarcoma (8), rhabdoid cancer (8), renal clear cell carcinoma (8), mucinous cystadenocarcinoma (7), villonodular synovitis (7), syringocystadenoma papilliferum (7), clear cell meningioma (7), gastrointestinal stromal tumor (7), astroblastoma (7), myxopapillary ependymoma (7), pseudosarcomatous fibromatosis (7), dermoid cyst (7), amelanotic melanoma (7), retroperitoneal fibrosis (7), benign mesothelioma (7), adenofibroma (7), large cell medulloblastoma (7), collecting duct carcinoma (7), perivascular epithelioid cell tumor (7), cutaneous fibrous histiocytoma (7), sarcoma, synovial (7), tay-sachs disease (7), epithelial-myoepithelial carcinoma (7), acral lentiginous melanoma (7), sarcomatoid mesothelioma (7), optic nerve glioma (7), tuberous sclerosis (7), dystonia-1, torsion (6), extraskeletal ewing sarcoma (6), syndrome of inappropriate antidiuretic hormone (6), endodermal sinus tumor (6), angiocentric glioma (6), adenosarcoma (6), odontoma (6), meningioma, familial (6), papillary adenocarcinoma (6), infantile myofibromatosis (6), spiradenoma (6), lymphangioma (6), fibrolamellar carcinoma (6), osteofibrous dysplasia (5), glossopharyngeal neuralgia (5), oxyphilic adenoma (5), peliosis hepatis (5), osteochondroma (5), focal hand dystonia (5), neurilemmoma (5), fasciitis (5), hidradenocarcinoma (5), chondromyxoid fibroma (4), pneumothorax (4), inflammatory myofibroblastic tumor (4), hemidystonia (4), dystonia-11, myoclonic (4), glossopharyngeal nerve disease (4), gliosarcoma (4), astrocytoma (3), renal cell carcinoma (3), ewing sarcoma (2), hepatitis c virus (2), mesothelioma, somatic (2), fanconi anemia, complementation group a (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1369.30 RPKM in Artery - Tibial
Total median expression: 17623.75 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -147.11413-0.356 Picture PostScript Text
3' UTR -60.85322-0.189 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016044 - F
IPR001664 - IF
IPR006821 - Intermed_filament_DNA-bd
IPR018039 - Intermediate_filament_CS

Pfam Domains:
PF00038 - Intermediate filament protein
PF04732 - Intermediate filament head (DNA binding) region

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1GK4
- X-ray MuPIT

1GK6
- X-ray

1GK7
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3G1E - X-ray 3KLT - X-ray MuPIT 3S4R - X-ray MuPIT
3SSU - X-ray MuPIT 3SWK - X-ray MuPIT 3TRT - X-ray MuPIT
3UF1 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P08670
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003725 double-stranded RNA binding
GO:0005198 structural molecule activity
GO:0005200 structural constituent of cytoskeleton
GO:0005212 structural constituent of eye lens
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0019904 protein domain specific binding
GO:0042802 identical protein binding
GO:0097110 scaffold protein binding
GO:1990254 keratin filament binding

Biological Process:
GO:0010628 positive regulation of gene expression
GO:0010977 negative regulation of neuron projection development
GO:0014002 astrocyte development
GO:0016032 viral process
GO:0019221 cytokine-mediated signaling pathway
GO:0030049 muscle filament sliding
GO:0032967 positive regulation of collagen biosynthetic process
GO:0043488 regulation of mRNA stability
GO:0045103 intermediate filament-based process
GO:0045109 intermediate filament organization
GO:0045727 positive regulation of translation
GO:0060020 Bergmann glial cell differentiation
GO:0060395 SMAD protein signal transduction
GO:0070307 lens fiber cell development
GO:0071346 cellular response to interferon-gamma

Cellular Component:
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005829 cytosol
GO:0005844 polysome
GO:0005856 cytoskeleton
GO:0005882 intermediate filament
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0031252 cell leading edge
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0045335 phagocytic vesicle
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  LQ740465 - Sequence 19 from Patent WO2018083189.
LF211788 - JP 2014500723-A/19291: Polycomb-Associated Non-Coding RNAs.
BC066956 - Homo sapiens vimentin, mRNA (cDNA clone MGC:87432 IMAGE:4823475), complete cds.
LF205547 - JP 2014500723-A/13050: Polycomb-Associated Non-Coding RNAs.
AK222507 - Homo sapiens mRNA for vimentin variant, clone: adSE00236.
AK222602 - Homo sapiens mRNA for vimentin variant, clone: CAS06773.
EU794672 - Homo sapiens epididymis luminal protein 113 (HEL113) mRNA, complete cds.
AK056766 - Homo sapiens cDNA FLJ32204 fis, clone PLACE6003077, highly similar to VIMENTIN.
AK091813 - Homo sapiens cDNA FLJ34494 fis, clone HLUNG2005030, highly similar to VIMENTIN.
AK097336 - Homo sapiens cDNA FLJ40017 fis, clone STOMA2006330, highly similar to VIMENTIN.
AK098444 - Homo sapiens cDNA FLJ25578 fis, clone JTH07876, highly similar to VIMENTIN.
X16478 - Human mRNA 5'-fragment for vimentin N-terminal fragment.
AK222482 - Homo sapiens mRNA for vimentin variant, clone: adKA02440.
AF328728 - Homo sapiens CTCL tumor antigen HD-CL-06 mRNA, complete sequence.
BC030573 - Homo sapiens vimentin, mRNA (cDNA clone MGC:16183 IMAGE:3637336), complete cds.
BC000163 - Homo sapiens vimentin, mRNA (cDNA clone MGC:5062 IMAGE:2985712), complete cds.
GQ900939 - Homo sapiens clone HEL-T-51 epididymis secretory sperm binding protein mRNA, complete cds.
Z19554 - Homo sapiens vimentin gene, clone vim6.
JD329678 - Sequence 310702 from Patent EP1572962.
JD069288 - Sequence 50312 from Patent EP1572962.
JD121854 - Sequence 102878 from Patent EP1572962.
LF346167 - JP 2014500723-A/153670: Polycomb-Associated Non-Coding RNAs.
X56134 - Human mRNA for vimentin.
AK290643 - Homo sapiens cDNA FLJ76120 complete cds, highly similar to Homo sapiens vimentin (VIM), mRNA.
JD209677 - Sequence 190701 from Patent EP1572962.
AB590763 - Synthetic construct DNA, clone: pFN21AE1928, Homo sapiens VIM gene for vimentin, without stop codon, in Flexi system.
CU674070 - Synthetic construct Homo sapiens gateway clone IMAGE:100017328 5' read VIM mRNA.
KJ892377 - Synthetic construct Homo sapiens clone ccsbBroadEn_01771 VIM gene, encodes complete protein.
CR407690 - Homo sapiens full open reading frame cDNA clone RZPDo834E033D for gene VIM, vimentin complete cds, without stopcodon.
KU178388 - Homo sapiens vimentin isoform 1 (VIM) mRNA, partial cds.
KU178389 - Homo sapiens vimentin isoform 2 (VIM) mRNA, complete cds, alternatively spliced.
LF346169 - JP 2014500723-A/153672: Polycomb-Associated Non-Coding RNAs.
LF346170 - JP 2014500723-A/153673: Polycomb-Associated Non-Coding RNAs.
LF346172 - JP 2014500723-A/153675: Polycomb-Associated Non-Coding RNAs.
LF346174 - JP 2014500723-A/153677: Polycomb-Associated Non-Coding RNAs.
M25246 - Human vimentin (HuVim3) mRNA, 3' end.
LF346175 - JP 2014500723-A/153678: Polycomb-Associated Non-Coding RNAs.
AK093924 - Homo sapiens cDNA FLJ36605 fis, clone TRACH2015316.
LF346177 - JP 2014500723-A/153680: Polycomb-Associated Non-Coding RNAs.
LF346179 - JP 2014500723-A/153682: Polycomb-Associated Non-Coding RNAs.
LF346181 - JP 2014500723-A/153684: Polycomb-Associated Non-Coding RNAs.
LF346183 - JP 2014500723-A/153686: Polycomb-Associated Non-Coding RNAs.
LF346185 - JP 2014500723-A/153688: Polycomb-Associated Non-Coding RNAs.
LF346186 - JP 2014500723-A/153689: Polycomb-Associated Non-Coding RNAs.
LF346187 - JP 2014500723-A/153690: Polycomb-Associated Non-Coding RNAs.
BC031031 - Homo sapiens vimentin, mRNA (cDNA clone IMAGE:4731764), partial cds.
LF346188 - JP 2014500723-A/153691: Polycomb-Associated Non-Coding RNAs.
JD428844 - Sequence 409868 from Patent EP1572962.
LF346189 - JP 2014500723-A/153692: Polycomb-Associated Non-Coding RNAs.
JD372311 - Sequence 353335 from Patent EP1572962.
JD373073 - Sequence 354097 from Patent EP1572962.
JD250901 - Sequence 231925 from Patent EP1572962.
MA581744 - JP 2018138019-A/153670: Polycomb-Associated Non-Coding RNAs.
MA581746 - JP 2018138019-A/153672: Polycomb-Associated Non-Coding RNAs.
MA581747 - JP 2018138019-A/153673: Polycomb-Associated Non-Coding RNAs.
MA581749 - JP 2018138019-A/153675: Polycomb-Associated Non-Coding RNAs.
MA581751 - JP 2018138019-A/153677: Polycomb-Associated Non-Coding RNAs.
MA581752 - JP 2018138019-A/153678: Polycomb-Associated Non-Coding RNAs.
MA581754 - JP 2018138019-A/153680: Polycomb-Associated Non-Coding RNAs.
MA581756 - JP 2018138019-A/153682: Polycomb-Associated Non-Coding RNAs.
MA581758 - JP 2018138019-A/153684: Polycomb-Associated Non-Coding RNAs.
MA581760 - JP 2018138019-A/153686: Polycomb-Associated Non-Coding RNAs.
MA581762 - JP 2018138019-A/153688: Polycomb-Associated Non-Coding RNAs.
MA581763 - JP 2018138019-A/153689: Polycomb-Associated Non-Coding RNAs.
MA581764 - JP 2018138019-A/153690: Polycomb-Associated Non-Coding RNAs.
MA581765 - JP 2018138019-A/153691: Polycomb-Associated Non-Coding RNAs.
MA581766 - JP 2018138019-A/153692: Polycomb-Associated Non-Coding RNAs.
MA447365 - JP 2018138019-A/19291: Polycomb-Associated Non-Coding RNAs.
MA441124 - JP 2018138019-A/13050: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P08670 (Reactome details) participates in the following event(s):

R-HSA-201628 Caspase-mediated cleavage of vimentin at DSVD (85)
R-HSA-350318 Caspase-mediated cleavage of vimentin at TNLD (429)
R-HSA-350319 Caspase mediated cleavage of vimentin at IDVD (259)
R-HSA-390595 Calcium Binds Troponin-C
R-HSA-390597 Release Of ADP From Myosin
R-HSA-390593 ATP Hydrolysis By Myosin
R-HSA-390598 Myosin Binds ATP
R-HSA-264870 Caspase-mediated cleavage of cytoskeletal proteins
R-HSA-6785807 Interleukin-4 and 13 signaling
R-HSA-111465 Apoptotic cleavage of cellular proteins
R-HSA-390522 Striated Muscle Contraction
R-HSA-449147 Signaling by Interleukins
R-HSA-75153 Apoptotic execution phase
R-HSA-397014 Muscle contraction
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-109581 Apoptosis
R-HSA-168256 Immune System
R-HSA-5357801 Programmed Cell Death

-  Other Names for This Gene
  Alternate Gene Symbols: B0YJC2, D3DRU4, NM_003380, NP_003371, P08670, Q15867, Q15868, Q15869, Q548L2, Q6LER9, Q8N850, Q96ML2, Q9NTM3, VIME_HUMAN
UCSC ID: uc001iou.2
RefSeq Accession: NM_003380
Protein: P08670 (aka VIME_HUMAN)
CCDS: CCDS7120.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003380.3
exon count: 10CDS single in 3' UTR: no RNA size: 2151
ORF size: 1401CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2728.00frame shift in genome: no % Coverage: 99.30
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.