VIM (vimentin) - Rat Genome Database

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Gene: VIM (vimentin) Canis lupus familiaris
Analyze
Symbol: VIM
Name: vimentin
RGD ID: 12074068
Description: ENCODES a protein that exhibits double-stranded RNA binding (ortholog); identical protein binding (ortholog); keratin filament binding (ortholog); INVOLVED IN astrocyte development (ortholog); Bergmann glial cell differentiation (ortholog); cellular response to fibroblast growth factor stimulus (ortholog); PARTICIPATES IN cyclooxygenase mediated pathway of arachidonic acid metabolism; ASSOCIATED WITH Acute Coronary Syndrome (ortholog); Alzheimer's disease (ortholog); amyotrophic lateral sclerosis type 1 (ortholog); FOUND IN axon (ortholog); cell body (ortholog); cell leading edge (ortholog); INTERACTS WITH ochratoxin A
Type: protein-coding
RefSeq Status: VALIDATED
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1219,671,316 - 19,679,367 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl219,671,316 - 19,679,466 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,774,615 - 16,782,665 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0219,962,890 - 19,970,942 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl219,941,383 - 19,970,947 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1217,165,331 - 17,173,380 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0218,003,247 - 18,011,326 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0218,621,519 - 18,629,571 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Coronary Syndrome  (ISO)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis type 1  (ISO)
Animal Disease Models  (ISO)
atherosclerosis  (ISO)
Behcet's disease  (ISO)
Brain Injuries  (ISO)
Breast Neoplasms  (ISO)
carcinosarcoma  (ISO)
cataract  (ISO)
cataract 30  (ISO)
cerebral infarction  (ISO)
Chagas disease  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
Chronic Intermittent Hypoxia  (ISO)
Closed Head Injuries  (ISO)
coronary artery disease  (ISO)
COVID-19  (ISO)
diabetes mellitus  (ISO)
Experimental Arthritis  (ISO)
Experimental Liver Cirrhosis  (ISO)
Experimental Liver Neoplasms  (ISO)
Fever  (ISO)
Fibrosis  (ISO)
genetic disease  (ISO)
Gliosis  (ISO)
hyperthyroidism  (ISO)
hypoparathyroidism-deafness-renal disease syndrome  (ISO)
Imerslund-Grasbeck Syndrome  (ISO)
kidney disease  (ISO)
liver cirrhosis  (ISO)
malignant mesothelioma  (ISO)
motor neuron disease  (ISO)
Neoplasm Invasiveness  (ISO)
Neoplasm Metastasis  (ISO)
Neoplastic Cell Transformation  (ISO)
nephrosis  (ISO)
neurodegenerative disease  (ISO)
osteoarthritis  (ISO)
Penetrating Head Injuries  (ISO)
Peritoneal Neoplasms  (ISO)
Prostatic Neoplasms  (ISO)
Pulmonary Arterial Hypertension  (ISO)
pulmonary hypertension  (ISO)
Reperfusion Injury  (ISO)
retinal disease  (ISO)
rheumatoid arthritis  (ISO)
severe acute respiratory syndrome  (ISO)
Sjogren's syndrome  (ISO)
Spinal Cord Injuries  (ISO)
synovial sarcoma  (ISO)
systemic lupus erythematosus  (ISO)
Urination Disorders  (ISO)
varicose veins  (ISO)
Vascular Remodeling  (ISO)
Weight Gain  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
ochratoxin A  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:15766329   PMID:16571866   PMID:19386766   PMID:19494238   PMID:22301074   PMID:22537462   PMID:22946050   PMID:25079702   PMID:30032202   PMID:37756605  


Genomics

Comparative Map Data
VIM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1219,671,316 - 19,679,367 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl219,671,316 - 19,679,466 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,774,615 - 16,782,665 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0219,962,890 - 19,970,942 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl219,941,383 - 19,970,947 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1217,165,331 - 17,173,380 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0218,003,247 - 18,011,326 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0218,621,519 - 18,629,571 (-)NCBIUU_Cfam_GSD_1.0
VIM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381017,228,241 - 17,237,593 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1017,228,241 - 17,237,593 (+)EnsemblGRCh38hg38GRCh38
GRCh371017,270,240 - 17,279,592 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361017,311,304 - 17,319,598 (+)NCBINCBI36Build 36hg18NCBI36
Build 341017,311,308 - 17,319,594NCBI
Celera1017,203,520 - 17,212,854 (+)NCBICelera
Cytogenetic Map10p13NCBI
HuRef1017,183,488 - 17,192,823 (+)NCBIHuRef
CHM1_11017,270,372 - 17,279,705 (+)NCBICHM1_1
T2T-CHM13v2.01017,246,786 - 17,256,137 (+)NCBIT2T-CHM13v2.0
Vim
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39213,579,122 - 13,587,637 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl213,578,738 - 13,587,637 (+)EnsemblGRCm39 Ensembl
GRCm38213,574,311 - 13,582,826 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl213,573,927 - 13,582,826 (+)EnsemblGRCm38mm10GRCm38
MGSCv37213,495,938 - 13,504,453 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36213,491,805 - 13,500,660 (+)NCBIMGSCv36mm8
Celera213,484,803 - 13,493,320 (+)NCBICelera
Cytogenetic Map2A1NCBI
cM Map210.04NCBI
Vim
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81781,577,261 - 81,585,746 (+)NCBIGRCr8
mRatBN7.21776,668,701 - 76,677,186 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1776,668,647 - 76,677,187 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1780,141,211 - 80,149,708 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01783,976,613 - 83,985,110 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01778,024,506 - 78,033,003 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01780,882,715 - 80,891,200 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1780,882,666 - 80,891,212 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01782,500,898 - 82,509,383 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41787,847,280 - 87,855,763 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11787,858,112 - 87,866,596 (+)NCBI
Celera1776,037,845 - 76,046,329 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
Vim
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542910,707,719 - 10,717,554 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542910,708,852 - 10,716,743 (-)NCBIChiLan1.0ChiLan1.0
VIM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2830,070,175 - 30,080,269 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11030,073,747 - 30,085,591 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01017,546,389 - 17,554,702 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11017,818,285 - 17,826,642 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1017,818,285 - 17,826,642 (+)Ensemblpanpan1.1panPan2
Vim
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934417,901,147 - 17,908,782 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493652010,052,012 - 10,059,182 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493652010,051,692 - 10,059,324 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VIM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1043,517,307 - 43,526,170 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11043,516,441 - 43,526,172 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21048,225,950 - 48,235,670 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VIM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1917,183,466 - 17,191,771 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl917,183,388 - 17,191,829 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605122,821,093 - 22,830,717 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vim
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479610,623,929 - 10,632,600 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479610,624,672 - 10,632,300 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VIM
134 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High 1 4 6 6 6
Medium 5 5 21 6 2 6 6 12 8 4
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSCAFT00000007304   ⟹   ENSCAFP00000006766
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,316 - 19,679,466 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000070460   ⟹   ENSCAFP00000065837
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,316 - 19,679,367 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000071494   ⟹   ENSCAFP00000057208
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,316 - 19,679,367 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000087931   ⟹   ENSCAFP00000050747
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,595 - 19,679,466 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000088846   ⟹   ENSCAFP00000044531
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,470 - 19,679,367 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024814   ⟹   ENSCAFP00845019520
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl219,941,383 - 19,970,947 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024849   ⟹   ENSCAFP00845019547
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl219,962,896 - 19,970,942 (-)Ensembl
RefSeq Acc Id: NM_001287023   ⟹   NP_001273952
RefSeq Status: VALIDATED
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1219,671,316 - 19,679,367 (-)NCBI
Dog10K_Boxer_Tasha216,774,615 - 16,782,665 (-)NCBI
ROS_Cfam_1.0219,962,890 - 19,970,942 (-)NCBI
UMICH_Zoey_3.1217,165,331 - 17,173,380 (-)NCBI
UNSW_CanFamBas_1.0218,003,247 - 18,011,326 (-)NCBI
UU_Cfam_GSD_1.0218,621,519 - 18,629,571 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001273952 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABO15561 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCAFP00000044531.2
  ENSCAFP00000057208.2
  ENSCAFP00000065837.2
  ENSCAFP00030020837.1
  ENSCAFP00845019520
  ENSCAFP00845019520.1
  ENSCAFP00845019547.1
RefSeq Acc Id: NP_001273952   ⟸   NM_001287023
- UniProtKB: A0A8C0K8U7 (UniProtKB/TrEMBL),   A0A8C0N8E3 (UniProtKB/TrEMBL),   A0A8I3NU02 (UniProtKB/TrEMBL),   A0A8I3NNR9 (UniProtKB/TrEMBL),   A0A8P0PEC2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000044531   ⟸   ENSCAFT00000088846
RefSeq Acc Id: ENSCAFP00000065837   ⟸   ENSCAFT00000070460
RefSeq Acc Id: ENSCAFP00000050747   ⟸   ENSCAFT00000087931
RefSeq Acc Id: ENSCAFP00000057208   ⟸   ENSCAFT00000071494
RefSeq Acc Id: ENSCAFP00000006766   ⟸   ENSCAFT00000007304
RefSeq Acc Id: ENSCAFP00845019547   ⟸   ENSCAFT00845024849
RefSeq Acc Id: ENSCAFP00845019520   ⟸   ENSCAFT00845024814
Protein Domains
IF rod

Promoters
RGD ID:13682398
Promoter ID:EPDNEW_C467
Type:multiple initiation site
Name:VIM_1
Description:vimentin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1219,679,373 - 19,679,433EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000004529 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030012938 UniProtKB/TrEMBL
  ENSCAFG00845013892 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000070460.2 UniProtKB/TrEMBL
  ENSCAFT00000071494.2 UniProtKB/TrEMBL
  ENSCAFT00000088846.2 UniProtKB/TrEMBL
  ENSCAFT00030023909.1 UniProtKB/TrEMBL
  ENSCAFT00845024814 ENTREZGENE
  ENSCAFT00845024814.1 UniProtKB/TrEMBL
  ENSCAFT00845024849.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/TrEMBL
  Single helix bin UniProtKB/TrEMBL
  Vasodilator-stimulated phosphoprotein UniProtKB/TrEMBL
InterPro IF_conserved UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/TrEMBL
  Intermed_filament_DNA-bd UniProtKB/TrEMBL
KEGG Report cfa:477991 UniProtKB/TrEMBL
NCBI Gene VIM ENTREZGENE
PANTHER GLIAL FIBRILLARY ACIDIC PROTEIN UniProtKB/TrEMBL
  PTHR45652:SF5 UniProtKB/TrEMBL
Pfam Filament UniProtKB/TrEMBL
  Filament_head UniProtKB/TrEMBL
PROSITE IF_ROD_1 UniProtKB/TrEMBL
  IF_ROD_2 UniProtKB/TrEMBL
SMART Filament UniProtKB/TrEMBL
Superfamily-SCOP Intermediate filament protein, coiled coil region UniProtKB/TrEMBL
UniProt A0A8C0K8U7 ENTREZGENE
  A0A8C0N8E3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NNR9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NU02 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0PEC2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0SXV1_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:48263 ENTREZGENE