Vcl (vinculin) - Rat Genome Database

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Gene: Vcl (vinculin) Rattus norvegicus
Analyze
Symbol: Vcl
Name: vinculin
RGD ID: 1311217
Description: Enables small GTPase binding activity. Predicted to be involved in several processes, including cell-cell junction assembly; platelet aggregation; and protein localization to cell surface. Predicted to act upstream of or within axon extension; lamellipodium assembly; and regulation of cell migration. Located in several cellular components, including Z disc; actin cytoskeleton; and focal adhesion. Human ortholog(s) of this gene implicated in dilated cardiomyopathy; dilated cardiomyopathy 1W; hypertrophic cardiomyopathy; and hypertrophic cardiomyopathy 15. Orthologous to human VCL (vinculin); PARTICIPATES IN E-cadherin signaling pathway; vascular endothelial growth factor signaling pathway; Entamoebiasis pathway; INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC305679; metavinculin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8153,315,069 - 3,404,891 (-)NCBIGRCr8
mRatBN7.2153,265,776 - 3,355,586 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx153,275,988 - 3,365,714 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0154,662,476 - 4,752,199 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0153,274,793 - 3,364,523 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0153,455,211 - 3,544,738 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl153,455,211 - 3,544,702 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0153,433,521 - 3,522,441 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,478,214 - 3,576,911 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1153,480,194 - 3,654,123 (-)NCBI
Celera151,235,777 - 1,325,408 (+)NCBICelera
Cytogenetic Map15p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
1,8-cineole  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-methoxyethanol  (EXP)
2-methylcholine  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
aniline  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
cadmium dichloride  (EXP)
caffeine  (ISO)
carbamazepine  (ISO)
CGP 52608  (ISO)
chloroprene  (EXP)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clozapine  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP,ISO)
diclofenac  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP)
fenamidone  (ISO)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
fructose  (EXP)
fumonisin B1  (ISO)
genistein  (ISO)
glucose  (ISO)
glycerol 2-phosphate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
griseofulvin  (ISO)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
hydroxychloroquine  (ISO)
imidacloprid  (EXP)
indometacin  (ISO)
ivermectin  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
methimazole  (EXP)
methotrexate  (ISO)
methoxychlor  (EXP)
microcystin RR  (ISO)
microcystin-LR  (EXP)
mifepristone  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
naphthalene  (ISO)
nickel atom  (ISO)
nitrofen  (EXP)
Nonylphenol  (ISO)
ozone  (EXP,ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
resveratrol  (ISO)
rimonabant  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium sulfide (anhydrous)  (ISO)
Soman  (EXP)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (EXP,ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
zearalenone  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. nArgBP2, a novel neural member of ponsin/ArgBP2/vinexin family that interacts with synapse-associated protein 90/postsynaptic density-95-associated protein (SAPAP). Kawabe H, etal., J Biol Chem 1999 Oct 22;274(43):30914-8.
4. A PLCdelta1-binding protein, p122RhoGAP, is localized in focal adhesions. Kawai K, etal., Biochem Soc Trans. 2004 Dec;32(Pt 6):1107-9.
5. Immunofluorescence localization of the Na-Ca exchanger in heart cells. Kieval RS, etal., Am J Physiol. 1992 Aug;263(2 Pt 1):C545-50.
6. Interaction between liprin-alpha and GIT1 is required for AMPA receptor targeting. Ko J, etal., J Neurosci. 2003 Mar 1;23(5):1667-77.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Identification of a metavinculin missense mutation, R975W, associated with both hypertrophic and dilated cardiomyopathy. Vasile VC, etal., Mol Genet Metab. 2006 Feb;87(2):169-74. Epub 2005 Oct 19.
Additional References at PubMed
PMID:7816144   PMID:9415431   PMID:9700171   PMID:11732910   PMID:12203715   PMID:12473693   PMID:14657280   PMID:15128702   PMID:15883197   PMID:16481394   PMID:16803572   PMID:17893324  
PMID:18341635   PMID:19056867   PMID:19116150   PMID:19725078   PMID:20086044   PMID:20458337   PMID:21048959   PMID:21423176   PMID:22871113   PMID:22984613   PMID:23382103   PMID:24036928  
PMID:24623780   PMID:24769233   PMID:25204797   PMID:25217619   PMID:25424202   PMID:25468996   PMID:25753039   PMID:26316108   PMID:26359501   PMID:26437238   PMID:26923917   PMID:29162887  
PMID:30354218   PMID:30502091   PMID:35352799  


Genomics

Comparative Map Data
Vcl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8153,315,069 - 3,404,891 (-)NCBIGRCr8
mRatBN7.2153,265,776 - 3,355,586 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx153,275,988 - 3,365,714 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0154,662,476 - 4,752,199 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0153,274,793 - 3,364,523 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0153,455,211 - 3,544,738 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl153,455,211 - 3,544,702 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0153,433,521 - 3,522,441 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,478,214 - 3,576,911 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1153,480,194 - 3,654,123 (-)NCBI
Celera151,235,777 - 1,325,408 (+)NCBICelera
Cytogenetic Map15p16NCBI
VCL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381073,998,116 - 74,121,363 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1073,995,193 - 74,121,363 (+)EnsemblGRCh38hg38GRCh38
GRCh371075,757,874 - 75,881,121 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361075,427,878 - 75,549,924 (+)NCBINCBI36Build 36hg18NCBI36
Build 341075,427,877 - 75,549,918NCBI
Celera1069,043,066 - 69,165,189 (+)NCBICelera
Cytogenetic Map10q22.2NCBI
HuRef1069,753,196 - 69,875,221 (+)NCBIHuRef
CHM1_11076,039,663 - 76,161,889 (+)NCBICHM1_1
T2T-CHM13v2.01074,869,505 - 74,992,765 (+)NCBIT2T-CHM13v2.0
Vcl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391420,979,436 - 21,083,744 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1420,979,466 - 21,083,744 (+)EnsemblGRCm39 Ensembl
GRCm381420,929,383 - 21,033,676 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1420,929,398 - 21,033,676 (+)EnsemblGRCm38mm10GRCm38
MGSCv371421,748,655 - 21,852,895 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361419,717,985 - 19,822,225 (+)NCBIMGSCv36mm8
Celera1417,309,615 - 17,412,913 (+)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1411.53NCBI
Vcl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543717,813,007 - 17,920,253 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543717,812,998 - 17,920,253 (-)NCBIChiLan1.0ChiLan1.0
VCL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2886,149,471 - 86,269,838 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11086,154,475 - 86,275,165 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01070,521,259 - 70,641,917 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11073,191,384 - 73,311,301 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1073,191,375 - 73,311,296 (+)Ensemblpanpan1.1panPan2
VCL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1424,404,279 - 24,518,977 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl424,404,319 - 24,518,633 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha424,541,842 - 24,656,546 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0424,685,066 - 24,802,488 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl424,685,097 - 24,802,479 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1424,581,947 - 24,697,844 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0424,782,214 - 24,897,783 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0425,137,362 - 25,252,305 (+)NCBIUU_Cfam_GSD_1.0
Vcl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721356,558,734 - 56,670,307 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365215,050,900 - 5,163,086 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365215,051,077 - 5,163,036 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VCL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1476,700,173 - 76,811,869 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11476,700,143 - 76,811,875 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21482,826,487 - 82,938,103 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap14q2.5-q2.9NCBI
VCL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1957,253,219 - 57,375,947 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl957,255,166 - 57,376,028 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604817,825,838 - 17,950,842 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vcl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247547,484,773 - 7,590,108 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247547,484,759 - 7,590,108 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vcl
405 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:288
Count of miRNA genes:178
Interacting mature miRNAs:225
Transcripts:ENSRNOT00000015179
Prediction methods: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
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat

Markers in Region
D15Got5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera151,243,608 - 1,243,802UniSTS
RH 3.4 Map1557.2RGD
RH 3.4 Map1557.2UniSTS
RH 2.0 Map150.0RGD
Cytogenetic Map15p16UniSTS
VCL  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,270,164 - 3,270,365 (+)MAPPERmRatBN7.2
Rnor_6.0153,459,600 - 3,459,800NCBIRnor6.0
Rnor_5.0153,437,910 - 3,438,110UniSTSRnor5.0
RGSC_v3.4153,482,603 - 3,482,803UniSTSRGSC3.4
Celera151,320,819 - 1,321,019UniSTS
Cytogenetic Map15p16UniSTS
RH133946  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,266,340 - 3,266,546 (+)MAPPERmRatBN7.2
Rnor_6.0153,455,776 - 3,455,981NCBIRnor6.0
Rnor_5.0153,434,086 - 3,434,291UniSTSRnor5.0
RGSC_v3.4153,478,779 - 3,478,984UniSTSRGSC3.4
Celera151,324,638 - 1,324,843UniSTS
RH 3.4 Map1563.2UniSTS
Cytogenetic Map15p16UniSTS
RH137914  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,266,846 - 3,266,983 (+)MAPPERmRatBN7.2
Rnor_6.0153,456,282 - 3,456,418NCBIRnor6.0
Rnor_5.0153,434,592 - 3,434,728UniSTSRnor5.0
RGSC_v3.4153,479,285 - 3,479,421UniSTSRGSC3.4
Celera151,324,201 - 1,324,337UniSTS
RH 3.4 Map1555.2UniSTS
Cytogenetic Map15p16UniSTS
RH139160  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,267,387 - 3,267,550 (+)MAPPERmRatBN7.2
Rnor_6.0153,456,823 - 3,456,985NCBIRnor6.0
Rnor_5.0153,435,133 - 3,435,295UniSTSRnor5.0
RGSC_v3.4153,479,826 - 3,479,988UniSTSRGSC3.4
Celera151,323,634 - 1,323,796UniSTS
RH 3.4 Map1563.9UniSTS
Cytogenetic Map15p16UniSTS
BARC0060  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2153,277,886 - 3,279,331 (+)MAPPERmRatBN7.2
Rnor_6.0153,467,322 - 3,468,766NCBIRnor6.0
Rnor_5.0153,445,632 - 3,447,076UniSTSRnor5.0
RGSC_v3.4153,491,109 - 3,492,553UniSTSRGSC3.4
Celera151,311,853 - 1,313,297UniSTS
Cytogenetic Map15p16UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000015179   ⟹   ENSRNOP00000015179
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)Ensembl
Rnor_6.0 Ensembl153,455,211 - 3,544,685 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000085126   ⟹   ENSRNOP00000074748
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)Ensembl
Rnor_6.0 Ensembl153,456,993 - 3,544,702 (-)Ensembl
RefSeq Acc Id: NM_001107248   ⟹   NP_001100718
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8153,315,069 - 3,404,800 (-)NCBI
mRatBN7.2153,265,776 - 3,355,523 (-)NCBI
Rnor_6.0153,455,211 - 3,544,685 (-)NCBI
Rnor_5.0153,433,521 - 3,522,441 (-)NCBI
RGSC_v3.4153,478,214 - 3,576,911 (-)RGD
Celera151,235,777 - 1,325,408 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251639   ⟹   XP_006251701
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8153,315,106 - 3,404,891 (-)NCBI
mRatBN7.2153,265,810 - 3,355,586 (-)NCBI
Rnor_6.0153,455,248 - 3,544,738 (-)NCBI
Rnor_5.0153,433,521 - 3,522,441 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001100718   ⟸   NM_001107248
- UniProtKB: A6KKR4 (UniProtKB/Swiss-Prot),   P85972 (UniProtKB/Swiss-Prot),   R9PXU6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251701   ⟸   XM_006251639
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000074748   ⟸   ENSRNOT00000085126
Ensembl Acc Id: ENSRNOP00000015179   ⟸   ENSRNOT00000015179

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P85972-F1-model_v2 AlphaFold P85972 1-1066 view protein structure

Transcriptome

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

Promoters
RGD ID:13699554
Promoter ID:EPDNEW_R10077
Type:multiple initiation site
Name:Vcl_1
Description:vinculin
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_6.0153,544,693 - 3,544,753EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311217 AgrOrtholog
BioCyc Gene G2FUF-14571 BioCyc
Ensembl Genes ENSRNOG00000010765 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055019101 UniProtKB/Swiss-Prot
  ENSRNOG00060012368 UniProtKB/Swiss-Prot
  ENSRNOG00065010245 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000015179 UniProtKB/TrEMBL
  ENSRNOT00000015179.8 UniProtKB/Swiss-Prot
  ENSRNOT00000085126.2 UniProtKB/TrEMBL
  ENSRNOT00055032594 UniProtKB/Swiss-Prot
  ENSRNOT00060021005 UniProtKB/Swiss-Prot
  ENSRNOT00065016529 UniProtKB/Swiss-Prot
Gene3D-CATH Alpha-catenin/vinculin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vinculin, Vh2 four-helix bundle UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Alpha-catenin/vinculin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vinculin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vinculin/catenin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vinculin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:305679 UniProtKB/Swiss-Prot
NCBI Gene 305679 ENTREZGENE
PANTHER PTHR46180 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VINCULIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Vinculin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vcl PhenoGen
PRINTS VINCULIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE VINCULIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VINCULIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010765 RatGTEx
  ENSRNOG00055019101 RatGTEx
  ENSRNOG00060012368 RatGTEx
  ENSRNOG00065010245 RatGTEx
Superfamily-SCOP SSF47220 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K8V2 ENTREZGENE, UniProtKB/TrEMBL
  A6KKR3 ENTREZGENE, UniProtKB/TrEMBL
  A6KKR4 ENTREZGENE
  P85972 ENTREZGENE
  R9PXU6 ENTREZGENE, UniProtKB/TrEMBL
  VINC_RAT UniProtKB/Swiss-Prot
UniProt Secondary A6KKR4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Vcl  vinculin   Vcl_predicted  vinculin (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Vcl_predicted  vinculin (predicted)      Symbol and Name status set to approved 70820 APPROVED