Vsnl1 (visinin-like 1) - Rat Genome Database
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Gene: Vsnl1 (visinin-like 1) Rattus norvegicus
Analyze
Symbol: Vsnl1
Name: visinin-like 1
RGD ID: 3966
Description: Predicted to have calcium ion binding activity. Predicted to be involved in negative regulation of insulin secretion; positive regulation of exocytosis; and positive regulation of insulin secretion involved in cellular response to glucose stimulus. Predicted to localize to cytosol and membrane. Orthologous to human VSNL1 (visinin like 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 21 kDa CABP; MGC105475; neural visinin-like protein 1; neurocalcin alpha; NVL-1; NVP-1; NVP1; RATNVP1; VILIP; visinin-like protein 1
Orthologs:
Homo sapiens (human) : VSNL1 (visinin like 1)  HGNC  Alliance
Mus musculus (house mouse) : Vsnl1 (visinin-like 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Vsnl1 (visinin like 1)
Pan paniscus (bonobo/pygmy chimpanzee) : VSNL1 (visinin like 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Vsnl1 (visinin like 1)
Sus scrofa (pig) : VSNL1 (visinin like 1)
Chlorocebus sabaeus (African green monkey) : VSNL1 (visinin like 1)
Heterocephalus glaber (naked mole-rat) : Vsnl1 (visinin like 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0637,001,360 - 37,121,969 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl637,001,356 - 37,122,023 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0646,751,473 - 46,872,211 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4634,770,053 - 34,895,220 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1634,773,006 - 34,898,173 (-)NCBI
Celera633,439,096 - 33,557,484 (-)NCBICelera
Cytogenetic Map6q15NCBI
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
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-methylcholine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-bromo-2'-deoxyuridine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
cadmium atom  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroquine  (EXP)
clozapine  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenamidone  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP)
genistein  (ISO)
haloperidol  (EXP)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
menadione  (ISO)
mercury dichloride  (EXP)
metformin  (EXP)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
nevirapine  (EXP)
nickel atom  (ISO)
O-methyleugenol  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
quercetin  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
titanium dioxide  (ISO)
tolcapone  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
uranium atom  (ISO)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (ISO)
membrane  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:11969245   PMID:12477932   PMID:15336574   PMID:15485673   PMID:16731532   PMID:18440708   PMID:18482800   PMID:18691652   PMID:18925431   PMID:20079378   PMID:22832524   PMID:22871113  
PMID:23707265   PMID:25451331   PMID:29476059  


Genomics

Comparative Map Data
Vsnl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0637,001,360 - 37,121,969 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl637,001,356 - 37,122,023 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0646,751,473 - 46,872,211 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4634,770,053 - 34,895,220 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1634,773,006 - 34,898,173 (-)NCBI
Celera633,439,096 - 33,557,484 (-)NCBICelera
Cytogenetic Map6q15NCBI
VSNL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl217,539,126 - 17,657,018 (+)EnsemblGRCh38hg38GRCh38
GRCh38217,539,972 - 17,657,018 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37217,721,807 - 17,837,706 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36217,585,288 - 17,701,187 (+)NCBINCBI36hg18NCBI36
Build 34217,643,597 - 17,759,331NCBI
Celera217,601,622 - 17,717,516 (+)NCBI
Cytogenetic Map2p24.2NCBI
HuRef217,496,887 - 17,612,808 (+)NCBIHuRef
CHM1_1217,651,208 - 17,767,107 (+)NCBICHM1_1
Vsnl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391211,375,258 - 11,486,579 (-)NCBI
GRCm381211,325,257 - 11,436,578 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1211,325,242 - 11,436,613 (-)EnsemblGRCm38mm10GRCm38
MGSCv371211,332,051 - 11,443,455 (-)NCBIGRCm37mm9NCBIm37
MGSCv361211,351,590 - 11,462,956 (-)NCBImm8
Celera1211,670,526 - 11,784,645 (-)NCBICelera
Cytogenetic Map12A1.1NCBI
Vsnl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955469350,983 - 454,264 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955469350,983 - 454,264 (+)NCBIChiLan1.0ChiLan1.0
VSNL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A17,651,535 - 17,767,274 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A17,703,086 - 17,767,274 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A17,525,561 - 17,641,277 (+)NCBIMhudiblu_PPA_v0panPan3
Vsnl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649313,258,420 - 13,362,190 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VSNL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3120,177,901 - 120,288,162 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13120,177,897 - 120,288,157 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23128,325,755 - 128,436,018 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VSNL1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1490,010,913 - 90,126,934 (-)Ensembl
ChlSab1.11490,012,733 - 90,127,994 (-)NCBI
Vsnl1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624738511,977 - 611,190 (+)NCBI

Position Markers
D6Arb7  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0637,002,270 - 37,002,488NCBIRnor6.0
Rnor_5.0646,752,383 - 46,752,601UniSTSRnor5.0
RGSC_v3.4634,770,963 - 34,771,181UniSTSRGSC3.4
RGSC_v3.4634,770,962 - 34,771,181RGDRGSC3.4
RGSC_v3.1634,773,915 - 34,774,134RGD
Celera633,440,006 - 33,440,224UniSTS
Cytogenetic Map6q14UniSTS
SHRSP x BN Map628.5599UniSTS
SHRSP x BN Map628.5599RGD
FHH x ACI Map629.35RGD
D6Rat38  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0637,002,238 - 37,002,388NCBIRnor6.0
Rnor_5.0646,752,351 - 46,752,501UniSTSRnor5.0
RGSC_v3.4634,770,930 - 34,771,081RGDRGSC3.4
RGSC_v3.4634,770,931 - 34,771,081UniSTSRGSC3.4
RGSC_v3.1634,773,841 - 34,774,159RGD
Celera633,439,974 - 33,440,124UniSTS
Cytogenetic Map6q14UniSTS
SHRSP x BN Map628.5599RGD
SHRSP x BN Map628.5599UniSTS
D6Arb5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0637,074,454 - 37,074,613NCBIRnor6.0
Rnor_5.0646,824,567 - 46,824,726UniSTSRnor5.0
RGSC_v3.4634,845,301 - 34,845,460UniSTSRGSC3.4
RGSC_v3.4634,845,300 - 34,845,460RGDRGSC3.4
RGSC_v3.1634,848,254 - 34,848,413RGD
Celera633,511,097 - 33,511,256UniSTS
Cytogenetic Map6q14UniSTS
RH 3.4 Map6143.6RGD
RH 3.4 Map6143.6UniSTS
RH 2.0 Map6296.4RGD
SHRSP x BN Map628.4898RGD
FHH x ACI Map629.28RGD
D6Got35  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0637,036,397 - 37,036,528NCBIRnor6.0
Rnor_5.0646,786,510 - 46,786,641UniSTSRnor5.0
RGSC_v3.4634,806,092 - 34,806,224RGDRGSC3.4
RGSC_v3.4634,806,093 - 34,806,224UniSTSRGSC3.4
RGSC_v3.1634,809,046 - 34,809,177RGD
Celera633,474,053 - 33,474,184UniSTS
Cytogenetic Map6q14UniSTS
RH 3.4 Map6142.3RGD
RH 3.4 Map6142.3UniSTS
RH139543  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0637,001,679 - 37,001,891NCBIRnor6.0
Rnor_5.0646,751,792 - 46,752,004UniSTSRnor5.0
RGSC_v3.4634,770,372 - 34,770,584UniSTSRGSC3.4
Celera633,439,415 - 33,439,627UniSTS
Cytogenetic Map6q14UniSTS
RH 3.4 Map6145.8UniSTS
RH140383  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0637,001,515 - 37,001,715NCBIRnor6.0
Rnor_5.0646,751,628 - 46,751,828UniSTSRnor5.0
RGSC_v3.4634,770,208 - 34,770,408UniSTSRGSC3.4
Celera633,439,251 - 33,439,451UniSTS
Cytogenetic Map6q14UniSTS
RH80046  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0637,001,653 - 37,001,840NCBIRnor6.0
Rnor_5.0646,751,766 - 46,751,953UniSTSRnor5.0
RGSC_v3.4634,770,346 - 34,770,533UniSTSRGSC3.4
Celera633,439,389 - 33,439,576UniSTS
Cytogenetic Map6q14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)percentage of deaths in a study population during a period of time (CMO:0001024)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)63425776653855198Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63626028860606186Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir25rno-miR-25-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir494rno-miR-494-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir374brno-miR-374-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir92a1rno-miR-92a-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir290rno-miR-290Mirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830

Predicted Target Of
Summary Value
Count of predictions:102
Count of miRNA genes:89
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000007609
Prediction methods:Miranda, Rnahybrid
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.


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 18 8 58 1 10
Low 2 24 27 19 17 19 8 10 10 24 35 1 8
Below cutoff 1 1 9 9 2 9 1 6 11 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012686 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07063602 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07063603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07063604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07063605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07063606 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07063607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042708 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01042710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC092197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D10666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000007609   ⟹   ENSRNOP00000007609
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl637,001,356 - 37,122,023 (-)Ensembl
RefSeq Acc Id: NM_012686   ⟹   NP_036818
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0637,001,360 - 37,121,969 (-)NCBI
Rnor_5.0646,751,473 - 46,872,211 (-)NCBI
RGSC_v3.4634,770,053 - 34,895,220 (-)RGD
Celera633,439,096 - 33,557,484 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036818 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH92197 (Get FASTA)   NCBI Sequence Viewer  
  BAA01517 (Get FASTA)   NCBI Sequence Viewer  
  EDM03102 (Get FASTA)   NCBI Sequence Viewer  
  EDM03103 (Get FASTA)   NCBI Sequence Viewer  
  P62762 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036818   ⟸   NM_012686
- UniProtKB: Q56A29 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007609   ⟸   ENSRNOT00000007609
Protein Domains
EF-hand

Transcriptome

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

Promoters
RGD ID:13694496
Promoter ID:EPDNEW_R5020
Type:multiple initiation site
Name:Vsnl1_1
Description:visinin-like 1
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_6.0637,121,966 - 37,122,026EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3966 AgrOrtholog
Ensembl Genes ENSRNOG00000005345 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000007609 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007609 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7313365 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Recoverin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VILIP-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24877 UniProtKB/TrEMBL
MGC_CLONE MGC:105475 IMAGE-MGC_LOAD
NCBI Gene 24877 ENTREZGENE
PANTHER PTHR23055 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR23055:SF101 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EF-hand_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand_7 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vsnl1 PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.105934 ENTREZGENE
UniProt P62762 ENTREZGENE
  Q56A29 ENTREZGENE, UniProtKB/TrEMBL
  VISL1_RAT UniProtKB/Swiss-Prot
UniProt Secondary P28677 UniProtKB/Swiss-Prot
  P29103 UniProtKB/Swiss-Prot
  P42323 UniProtKB/Swiss-Prot
  Q9UM20 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2001-07-23 Vsnl1  visinin-like 1      Name updated to reflect Human and Mouse nomenclature 67952 APPROVED
2001-07-23 Vsnl1  Neural visinin-like protein 1      Name withdrawn 67952 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in cerebellar granule cells 727467
gene_product member of the family of neuronal calcium sensor (NCS) proteins 727467