VIM (vimentin) - Rat Genome Database

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Gene: VIM (vimentin) Canis lupus familiaris
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Symbol: VIM
Name: vimentin
RGD ID: 12074068
Description: ENCODES a protein that exhibits kinase binding (ortholog); molecular adaptor activity (ortholog); protein phosphatase 2A binding (ortholog); INVOLVED IN aging (ortholog); astrocyte development (ortholog); Bergmann glial cell differentiation (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 (-)NCBI
ROS_Cfam_1.0219,962,890 - 19,970,942 (-)NCBI
ROS_Cfam_1.0 Ensembl219,941,383 - 19,970,947 (-)Ensembl
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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:22537462   PMID:22946050   PMID:25079702  


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 (-)NCBI
ROS_Cfam_1.0219,962,890 - 19,970,942 (-)NCBI
ROS_Cfam_1.0 Ensembl219,941,383 - 19,970,947 (-)Ensembl
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
VIM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381017,228,241 - 17,237,593 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1017,228,241 - 17,237,593 (+)EnsemblGRCh38hg38GRCh38
GRCh371017,270,240 - 17,279,592 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361017,311,304 - 17,319,598 (+)NCBINCBI36hg18NCBI36
Build 341017,311,308 - 17,319,594NCBI
Celera1017,203,520 - 17,212,854 (+)NCBI
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 (+)NCBI
Vim
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39213,579,122 - 13,587,637 (+)NCBIGRCm39mm39
GRCm39 Ensembl213,578,738 - 13,587,637 (+)Ensembl
GRCm38213,574,311 - 13,582,826 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl213,573,927 - 13,582,826 (+)EnsemblGRCm38mm10GRCm38
MGSCv37213,495,938 - 13,504,453 (+)NCBIGRCm37mm9NCBIm37
MGSCv36213,491,805 - 13,500,660 (+)NCBImm8
Celera213,484,803 - 13,493,320 (+)NCBICelera
Cytogenetic Map2A1NCBI
cM Map210.04NCBI
Vim
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21776,668,701 - 76,677,186 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1776,668,647 - 76,677,187 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
PanPan1.11017,818,285 - 17,826,642 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1017,818,285 - 17,826,642 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01017,546,389 - 17,554,702 (+)NCBIMhudiblu_PPA_v0panPan3
Vim
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934417,901,147 - 17,908,782 (+)NCBI
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 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl917,183,388 - 17,191,829 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605122,821,093 - 22,830,717 (+)NCBIVero_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_1.0hetGla2
HetGla 1.0NW_00462479610,624,672 - 10,632,300 (-)NCBIHetGla_female_1.0hetGla2


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


Reference Sequences
RefSeq Acc Id: ENSCAFT00000007304   ⟹   ENSCAFP00000006766
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,316 - 19,679,466 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000070460   ⟹   ENSCAFP00000065837
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,316 - 19,679,367 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000071494   ⟹   ENSCAFP00000057208
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,316 - 19,679,367 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000087931   ⟹   ENSCAFP00000050747
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,595 - 19,679,466 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000088846   ⟹   ENSCAFP00000044531
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl219,671,470 - 19,679,367 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024814   ⟹   ENSCAFP00845019520
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl219,941,383 - 19,970,947 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024849   ⟹   ENSCAFP00845019547
RefSeq Status:
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  
Reference Sequences
RefSeq Acc Id: NP_001273952   ⟸   NM_001287023
- UniProtKB: F1PLS4 (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
Damaging Variants


Assembly: CanFam3.1

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 19679169 19679170 C G snv Doberman Pinscher (DO159)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000004529 Ensembl
  ENSCAFG00030012938 UniProtKB/TrEMBL
  ENSCAFG00845013892 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSCAFP00030020837.1 UniProtKB/TrEMBL
  ENSCAFP00845019520 ENTREZGENE
  ENSCAFP00845019520.1 UniProtKB/TrEMBL
  ENSCAFP00845019547.1 UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00030023909.1 UniProtKB/TrEMBL
  ENSCAFT00845024814 ENTREZGENE
  ENSCAFT00845024814.1 UniProtKB/TrEMBL
  ENSCAFT00845024849.1 UniProtKB/TrEMBL
InterPro IF_conserved UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/TrEMBL
  Intermed_filament_DNA-bd UniProtKB/TrEMBL
  Vimentin UniProtKB/TrEMBL
NCBI Gene VIM ENTREZGENE
PANTHER 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
UniProt A0A8C0N8E3_CANLF UniProtKB/TrEMBL
  A0A8I3NNR9_CANLF UniProtKB/TrEMBL
  A0A8I3NU02_CANLF UniProtKB/TrEMBL
  F1PLS4 ENTREZGENE
VGNC ID VGNC:48263 ENTREZGENE