Vim vimentin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vimprovided by RGD
Official Full Name: vimentinprovided by RGD
Primary source: RGD:621646
See related: Ensembl:ENSRNOG00000018087 AllianceGenome:RGD:621646
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables protein kinase binding activity and protein phosphatase 2A binding activity. Involved in several processes, including decidualization; positive regulation of glial cell proliferation; and response to vitamin D. Located in several cellular components, including axon; cell body; and perinuclear region of cytoplasm. Biomarker of Chagas disease; cerebral infarction; hyperthyroidism; nephrosis; and pulmonary hypertension. Human ortholog(s) of this gene implicated in atherosclerosis; autoimmune disease (multiple); and cataract 30. Orthologous to human VIM (vimentin). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 2096.9), Heart (RPKM 1548.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17q12.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (81577261..81585746)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (76668701..76677186)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (80882715..80891200)

Chromosome 17 - NC_086035.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Impairment of Assembly of the Vimentin Intermediate Filaments Leads to Suppression of Formation and Maturation of Focal Contacts and Alteration of the Type of Cellular Protrusions.
Title: Impairment of Assembly of the Vimentin Intermediate Filaments Leads to Suppression of Formation and Maturation of Focal Contacts and Alteration of the Type of Cellular Protrusions.
The role of vimentin in directional migration of rat fibroblasts.
Title: The role of vimentin in directional migration of rat fibroblasts.
Delayed elevation in spinal astrocytic vimentin corresponds to sustained mechanical hyperalgesia.
Title: Nerve Root Compression Increases Spinal Astrocytic Vimentin in Parallel With Sustained Pain and Endothelial Vimentin in Association With Spinal Vascular Reestablishment.
We labeled brain with ZO1, vimentin, pan-cadherin and angiotensin II type 1 receptors markers which showed a morphologically distinct population of cells at the region of the sulcus medianus organum similar to tanycytes present in the median eminence, a known circumventricular organ.
Title: Expression of ZO1, vimentin, pan-cadherin and AGTR1 in tanycyte-like cells of the sulcus medianus organum.
The present study found that social isolation during adolescence resulted in abnormal locomotor, emotional and cognitive behaviors and increased the expression of GFAP, ANXA2 and VIM in PFC of adult rats.
Title: Adolescent social isolation affects schizophrenia-like behavior and astrocyte biomarkers in the PFC of adult rats.
dephosphorylation of MAP2D at Thr256 and Thr259, phosphorylation of vimentin at Ser38 and Ser72, and the resulting enhanced binding of MAP2D to vimentin might contribute to the progesterone synthetic response required for ovulation.
Title: Dephosphorylation of MAP2D enhances its binding to vimentin in preovulatory ovarian granulosa cells.
alpha-catulin has a unique function in co-localization with vimentin filaments that contributes to vascular endothelial cells migration via a pathway that may involve ROCK signaling.
Title: Alpha-Catulin Co-Localizes With Vimentin Intermediate Filaments and Functions in Pulmonary Vascular Endothelial Cell Migration via ROCK.
considering the steroid hormone imbalance in late life period, as well as, the role of this imbalance in prostatic lesion development and progression, the aim of the study herein was to characterize and correlate prolactin, EGFR, alpha-actin and vimentin immunoreactivity in the prostatic epithelium and stroma of elderly rats, following steroid hormone imbalance.
Title: Prolactin, EGFR, vimentin and α-actin profiles in elderly rat prostate subjected to steroid hormonal imbalance.
vimentin may be a novel ligand of IGF1R that promotes axonal growth in a similar manner to IGF1.
Title: Extracellular vimentin interacts with insulin-like growth factor 1 receptor to promote axonal growth.
In transected spinal cord rats, vimentin knockdown in the scar tissues showed a significant improvement on locomotor function in hindlimbs.
Title: Vimentin regulates neuroplasticity in transected spinal cord rats associated with micRNA138.

Submit: New GeneRIF Correction See all GeneRIFs (41)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Vim (e-PCR), detects polymorphism
- UniSTS:547844

VIM (e-PCR)
- UniSTS:253717

MARC_31619-31620:1062167711:1 (e-PCR)
- UniSTS:269211

Vim (e-PCR), detects polymorphism
- UniSTS:461982

VIM (e-PCR)
- UniSTS:527007

Vim (e-PCR), detects polymorphism
- UniSTS:527007

Vim (e-PCR), detects polymorphism
- UniSTS:507308

RH138541 (e-PCR)
- UniSTS:220628

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded RNA binding	IEA Inferred from Electronic Annotation more info
enables double-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables keratin filament binding	IEA Inferred from Electronic Annotation more info
enables keratin filament binding	ISO Inferred from Sequence Orthology more info
enables kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein phosphatase 2A binding	IDA Inferred from Direct Assay more info	PubMed
enables protein tyrosine kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables scaffold protein binding	IEA Inferred from Electronic Annotation more info
enables scaffold protein binding	ISO Inferred from Sequence Orthology more info
enables structural constituent of cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of cytoskeleton	IEA Inferred from Electronic Annotation more info
enables structural constituent of cytoskeleton	ISO Inferred from Sequence Orthology more info
enables structural constituent of cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
enables structural constituent of eye lens	IEA Inferred from Electronic Annotation more info
enables structural constituent of eye lens	ISO Inferred from Sequence Orthology more info
enables structural molecule activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in Bergmann glial cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Bergmann glial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in astrocyte development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within astrocyte development	ISO Inferred from Sequence Orthology more info
involved_in cellular response to fibroblast growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to muramyl dipeptide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to muramyl dipeptide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to muramyl dipeptide	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to type II interferon	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to type II interferon	ISO Inferred from Sequence Orthology more info
involved_in decidualization	IEP Inferred from Expression Pattern more info	PubMed
involved_in fat cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in intermediate filament organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in intermediate filament organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within intermediate filament organization	ISO Inferred from Sequence Orthology more info
involved_in intermediate filament organization	ISO Inferred from Sequence Orthology more info
involved_in intermediate filament organization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within intermediate filament-based process	ISO Inferred from Sequence Orthology more info
involved_in lens fiber cell development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lens fiber cell development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in neuron projection development	IEA Inferred from Electronic Annotation more info
acts_upstream_of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of collagen biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of collagen biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of glial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of Schwann cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of axonogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of mRNA stability	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA stability	ISO Inferred from Sequence Orthology more info
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to selenium ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to vitamin D	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to zinc ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in skeletal muscle tissue regeneration	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cell body	IDA Inferred from Direct Assay more info	PubMed
located_in cell leading edge	IEA Inferred from Electronic Annotation more info
located_in cell leading edge	ISO Inferred from Sequence Orthology more info
located_in cell projection	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in intermediate filament	IBA Inferred from Biological aspect of Ancestor more info
located_in intermediate filament	IEA Inferred from Electronic Annotation more info
located_in intermediate filament	ISO Inferred from Sequence Orthology more info
located_in intermediate filament	ISS Inferred from Sequence or Structural Similarity more info
located_in intermediate filament cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in nuclear matrix	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in peroxisome	IEA Inferred from Electronic Annotation more info
located_in peroxisome	ISO Inferred from Sequence Orthology more info
located_in phagocytic vesicle	IEA Inferred from Electronic Annotation more info
located_in phagocytic vesicle	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in type III intermediate filament	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: vimentin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_031140.1 → NP_112402.1 vimentin

See identical proteins and their annotated locations for NP_112402.1

Status: PROVISIONAL

Source sequence(s)

X62952

UniProtKB/Swiss-Prot

P31000

UniProtKB/TrEMBL

G3V8C3

Related

ENSRNOP00000024430.5, ENSRNOT00000024430.6

Conserved Domains (3) summary

pfam00038
Location:102 → 410

Filament; Intermediate filament protein

pfam04732
Location:14 → 101

Filament_head; Intermediate filament head (DNA binding) region

pfam15112
Location:153 → 257

DUF4559; Domain of unknown function (DUF4559)