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; protein localization to cell surface; and regulation of establishment of endothelial barrier. 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8153,315,069 - 3,404,891 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl153,315,069 - 3,405,163 (-)EnsemblGRCr8
mRatBN7.2153,265,776 - 3,355,586 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx153,275,988 - 3,365,714 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0154,662,476 - 4,752,199 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0153,274,793 - 3,364,523 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0153,455,211 - 3,544,738 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl153,455,211 - 3,544,702 (-)Ensemblrn6Rnor6.0
Rnor_5.0153,433,521 - 3,522,441 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4153,478,214 - 3,576,911 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera151,235,777 - 1,325,408 (+)NCBICelera
RGSC_v3.1153,480,194 - 3,654,123 (-)NCBI
Cytogenetic Map15p16NCBI
JBrowse:




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-dimethoxyphenol  (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 AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
Bufotalin  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium dichloride  (EXP,ISO)
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)
dimethyl sulfoxide  (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)
furfural  (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-ethyl-5-hydroxyhexyl) phthalate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
naphthalene  (ISO)
nickel atom  (ISO)
nitrofen  (EXP)
Nonylphenol  (ISO)
okadaic acid  (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 chloride  (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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl153,315,069 - 3,405,163 (-)EnsemblGRCr8
mRatBN7.2153,265,776 - 3,355,586 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl153,265,815 - 3,355,606 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx153,275,988 - 3,365,714 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0154,662,476 - 4,752,199 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0153,274,793 - 3,364,523 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0153,455,211 - 3,544,738 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl153,455,211 - 3,544,702 (-)Ensemblrn6Rnor6.0
Rnor_5.0153,433,521 - 3,522,441 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4153,478,214 - 3,576,911 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera151,235,777 - 1,325,408 (+)NCBICelera
RGSC_v3.1153,480,194 - 3,654,123 (-)NCBI
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 (+)Ensemblhg38GRCh38
GRCh371075,757,874 - 75,881,121 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361075,427,878 - 75,549,924 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381420,929,383 - 21,033,676 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1420,929,398 - 21,033,676 (+)Ensemblmm10GRCm38
MGSCv371421,748,655 - 21,852,895 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha424,541,842 - 24,656,546 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0424,685,066 - 24,802,488 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247547,484,759 - 7,590,108 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vcl
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11290,736,617 - 90,826,319 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vcl
363 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
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)15231575947315759Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15139411584Rat
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15132342855Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
1300142Bp191Blood pressure QTL 1913.14arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)15115177511Rat

Markers in Region
D15Got5  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8153,396,691 - 3,396,893 (+)Marker Load Pipeline
Celera151,243,608 - 1,243,802UniSTS
RH 3.4 Map1557.2UniSTS
RH 3.4 Map1557.2RGD
RH 2.0 Map150.0RGD
Cytogenetic Map15p16UniSTS
VCL  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8153,319,458 - 3,319,658 (+)Marker Load Pipeline
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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
18 13 78 176 91 90 59 138 59 6 436 251 13 162 100 108 31 22 22

Sequence


Ensembl Acc Id: ENSRNOT00000015179   ⟹   ENSRNOP00000015179
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl153,315,069 - 3,405,163 (-)Ensembl
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
GRCr8 Ensembl153,315,069 - 3,405,163 (-)Ensembl
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, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000015179 ENTREZGENE
  ENSRNOT00000015179.8 UniProtKB/Swiss-Prot
  ENSRNOT00000085126 ENTREZGENE
Gene3D-CATH Alpha-catenin/vinculin-like UniProtKB/Swiss-Prot
  Vinculin, Vh2 four-helix bundle UniProtKB/Swiss-Prot
InterPro Alpha-catenin/vinculin-like_sf UniProtKB/Swiss-Prot
  Vinculin UniProtKB/Swiss-Prot
  Vinculin/catenin UniProtKB/Swiss-Prot
  Vinculin_CS UniProtKB/Swiss-Prot
KEGG Report rno:305679 UniProtKB/Swiss-Prot
NCBI Gene 305679 ENTREZGENE
PANTHER PTHR46180 UniProtKB/Swiss-Prot
Pfam Vinculin UniProtKB/Swiss-Prot
PhenoGen Vcl PhenoGen
PRINTS VINCULIN UniProtKB/Swiss-Prot
PROSITE VINCULIN_1 UniProtKB/Swiss-Prot
  VINCULIN_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000010765 RatGTEx
Superfamily-SCOP SSF47220 UniProtKB/Swiss-Prot
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