Vmac (vimentin-type intermediate filament associated coiled-coil protein) - Rat Genome Database

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Gene: Vmac (vimentin-type intermediate filament associated coiled-coil protein) Rattus norvegicus
Analyze
Symbol: Vmac
Name: vimentin-type intermediate filament associated coiled-coil protein
RGD ID: 1303340
Description: Located in cytoplasm and type III intermediate filament. Orthologous to human VMAC (vimentin type intermediate filament associated coiled-coil protein); INTERACTS WITH acetamide; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: vimentin-type intermediate filament-associated coiled-coil protein
RGD Orthologs
Human
Mouse
Chinchilla
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.291,546,747 - 1,550,417 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,546,747 - 1,549,771 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,982,464 - 1,983,718 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.097,331,550 - 7,332,804 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.096,287,661 - 6,288,915 (-)NCBIRnor_WKY
Rnor_6.0910,338,260 - 10,341,903 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,339,075 - 10,340,329 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,335,290 - 9,338,983 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,967,173 - 6,968,428 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
protein binding  (IPI,ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Vmac: a novel protein associated with vimentin-type intermediate filament in podocytes of rat kidney. Yamamoto Y, etal., Biochem Biophys Res Commun 2004 Mar 19;315(4):1120-5.

Genomics

Comparative Map Data
Vmac
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.291,546,747 - 1,550,417 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,546,747 - 1,549,771 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,982,464 - 1,983,718 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.097,331,550 - 7,332,804 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.096,287,661 - 6,288,915 (-)NCBIRnor_WKY
Rnor_6.0910,338,260 - 10,341,903 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,339,075 - 10,340,329 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,335,290 - 9,338,983 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,967,173 - 6,968,428 (+)NCBICelera
Cytogenetic Map9q12NCBI
VMAC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38195,904,872 - 5,910,853 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl195,904,872 - 5,910,853 (+)EnsemblGRCh38hg38GRCh38
GRCh37195,904,883 - 5,910,864 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36195,855,894 - 5,861,263 (+)NCBINCBI36Build 36hg18NCBI36
Celera195,843,814 - 5,849,226 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef195,664,330 - 5,669,752 (+)NCBIHuRef
CHM1_1195,905,105 - 5,910,518 (+)NCBICHM1_1
T2T-CHM13v2.0195,892,302 - 5,898,294 (+)NCBIT2T-CHM13v2.0
Vmac
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391757,020,932 - 57,024,699 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1757,020,936 - 57,025,022 (-)EnsemblGRCm39 Ensembl
GRCm381756,713,932 - 56,717,699 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,713,936 - 56,718,022 (-)EnsemblGRCm38mm10GRCm38
MGSCv371756,853,355 - 56,857,122 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361756,399,062 - 56,401,976 (-)NCBIMGSCv36mm8
Celera1761,058,067 - 61,061,834 (-)NCBICelera
Cytogenetic Map17DNCBI
Vmac
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554953,554,567 - 3,555,973 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554953,553,025 - 3,556,726 (-)NCBIChiLan1.0ChiLan1.0
VMAC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12054,179,302 - 54,182,607 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2054,180,902 - 54,182,571 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2053,922,805 - 53,926,072 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02054,830,492 - 54,833,760 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12053,896,895 - 53,900,160 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02054,345,763 - 54,349,024 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02054,575,932 - 54,579,199 (-)NCBIUU_Cfam_GSD_1.0
Vmac
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,440,117 - 214,444,298 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365883,391,140 - 3,394,596 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365883,391,116 - 3,394,642 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VMAC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.165,525,250 - 5,525,993 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl65,525,271 - 5,525,585 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660812,501,115 - 2,506,868 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vmac
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248284,316,530 - 4,318,589 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248284,314,968 - 4,319,222 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vmac
8 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:91
Count of miRNA genes:68
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000073402
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat


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 renal system reproductive system respiratory system appendage
High
Medium 1 10 1 8 1 13 25 29 10
Low 3 42 47 40 11 40 8 11 61 10 12 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000073402   ⟹   ENSRNOP00000067724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl910,339,075 - 10,340,329 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109435   ⟹   ENSRNOP00000096954
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,546,747 - 1,549,771 (-)Ensembl
RefSeq Acc Id: NM_001001720   ⟹   NP_001001720
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,548,321 - 1,549,575 (-)NCBI
Rnor_6.0910,339,075 - 10,340,329 (+)NCBI
Rnor_5.099,335,290 - 9,338,983 (+)NCBI
Celera96,967,173 - 6,968,428 (+)RGD
Sequence:
RefSeq Acc Id: XM_008766765   ⟹   XP_008764987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,546,747 - 1,550,417 (-)NCBI
Rnor_6.0910,338,260 - 10,341,903 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766766   ⟹   XP_008764988
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,546,747 - 1,549,672 (-)NCBI
Rnor_6.0910,338,962 - 10,341,903 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001001720   ⟸   NM_001001720
- UniProtKB: Q6QZQ4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008764987   ⟸   XM_008766765
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008764988   ⟸   XM_008766766
- Peptide Label: isoform X2
- UniProtKB: A0A8I6ARR3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067724   ⟸   ENSRNOT00000073402
RefSeq Acc Id: ENSRNOP00000096954   ⟸   ENSRNOT00000109435

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6QZQ4-F1-model_v2 AlphaFold Q6QZQ4 1-171 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696453
Promoter ID:EPDNEW_R6978
Type:multiple initiation site
Name:Vmac_1
Description:vimentin-type intermediate filament associated coiled-coil protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0910,339,050 - 10,339,110EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303340 AgrOrtholog
BioCyc Gene G2FUF-28517 BioCyc
Ensembl Genes ENSRNOG00000048897 Ensembl
  ENSRNOG00000065863 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000096954 ENTREZGENE
  ENSRNOP00000096954.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000109435 ENTREZGENE
  ENSRNOT00000109435.1 UniProtKB/TrEMBL
InterPro VMAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:363327 UniProtKB/Swiss-Prot
NCBI Gene 363327 ENTREZGENE
PANTHER PTHR34707:SF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vmac PhenoGen
UniProt A0A8I6ARR3 ENTREZGENE, UniProtKB/TrEMBL
  Q6QZQ4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-14 Vmac  vimentin-type intermediate filament associated coiled-coil protein      Symbol and Name status set to provisional 70820 PROVISIONAL