Vsnl1 (visinin-like 1) - Rat Genome Database

Name: Vsnl1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Vsnl1 (visinin-like 1) Rattus norvegicus

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Symbol:

Vsnl1

Name:

visinin-like 1

RGD ID:

3966

Description:

Predicted to enable calcium ion binding activity. Predicted to be involved in calcium-mediated signaling and central nervous system development. Predicted to act upstream of or within negative regulation of insulin secretion; positive regulation of exocytosis; and positive regulation of insulin secretion involved in cellular response to glucose stimulus. Predicted to be located in cytosol and membrane. Orthologous to human VSNL1 (visinin like 1); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

21 kDa CABP; MGC105475; neural visinin-like protein 1; neurocalcin alpha; NVL-1; NVP-1; NVP1; RATNVP1; VILIP; visinin-like protein 1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	VSNL1 (visinin like 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Vsnl1 (visinin-like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Vsnl1 (visinin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	VSNL1 (visinin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	VSNL1 (visinin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Vsnl1 (visinin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	VSNL1 (visinin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	VSNL1 (visinin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Vsnl1 (visinin like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	HPCAL4 (hippocalcin like 4)	HGNC	OrthoDB
Homo sapiens (human):	TBP (TATA-box binding protein)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	VSNL1 (visinin like 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Vsnl1 (visinin-like 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	vsnl1a (visinin-like 1a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	vsnl1b (visinin-like 1b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	FRQ1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|PANTHER)
Drosophila melanogaster (fruit fly):	CG7646	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	vsnl1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	39,757,721 - 39,878,556 (-)	NCBI		GRCr8
mRatBN7.2	6	34,038,641 - 34,159,479 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	34,038,642 - 34,159,479 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	34,331,181 - 34,454,334 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	34,647,122 - 34,770,275 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	34,117,901 - 34,242,539 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	37,001,360 - 37,121,969 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	37,001,356 - 37,122,023 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	46,751,473 - 46,872,211 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	34,770,053 - 34,895,220 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	34,773,006 - 34,898,173 (-)	NCBI
Celera	6	33,439,096 - 33,557,484 (-)	NCBI		Celera
Cytogenetic Map	6	q15	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Alzheimer's disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1-chloro-2,4-dinitrobenzene (ISO)

17beta-estradiol (EXP,ISO)

17beta-estradiol 3-benzoate (EXP)

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)

alpha-Zearalanol (EXP)

ammonium chloride (EXP)

aristolochic acid A (ISO)

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)

cadmium dichloride (ISO)

calcitriol (ISO)

cannabidiol (ISO)

carbon nanotube (ISO)

CGP 52608 (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)

fulvestrant (ISO)

genistein (ISO)

haloperidol (EXP)

hydrogen peroxide (ISO)

hydroquinone (ISO)

ivermectin (ISO)

lead(0) (ISO)

leflunomide (ISO)

lipopolysaccharide (ISO)

menadione (ISO)

mercury dichloride (EXP)

metformin (EXP)

methapyrilene (ISO)

methylmercury chloride (ISO)

nevirapine (EXP)

nickel atom (ISO)

nitrofen (EXP)

O-methyleugenol (ISO)

ozone (ISO)

paracetamol (EXP,ISO)

paraquat (EXP)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (EXP,ISO)

phenylmercury acetate (ISO)

phorbol 13-acetate 12-myristate (ISO)

poly(I:C) (EXP)

quercetin (ISO)

rotenone (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

temozolomide (ISO)

tert-butyl hydroperoxide (ISO)

testosterone (EXP)

Theaflavin 3,3'-digallate (ISO)

thiram (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

Biological Process

calcium-mediated signaling (TAS)

central nervous system development (TAS)

negative regulation of insulin secretion (ISO)

positive regulation of exocytosis (ISO)

positive regulation of insulin secretion involved in cellular response to glucose stimulus (ISO)

Cellular Component

cytosol (ISO)

membrane (ISO)

Molecular Function

calcium ion binding (IBA,TAS)

protein binding (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.	cDNA cloning of a neural visinin-like Ca(2+)-binding protein.	Kuno T, etal., Biochem Biophys Res Commun 1992 May 15;184(3):1219-25.
3.	The calcium sensor protein visinin-like protein-1 modulates the surface expression and agonist sensitivity of the alpha 4beta 2 nicotinic acetylcholine receptor.	Lin L, etal., J Biol Chem 2002 Nov 1;277(44):41872-8.
4.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
6.	Calcium-myristoyl switch, subcellular localization, and calcium-dependent translocation of the neuronal calcium sensor protein VILIP-3, and comparison with VILIP-1 in hippocampal neurons.	Spilker C and Braunewell KH, Mol Cell Neurosci 2003 Nov;24(3):766-78.
7.	Evidence for different functional properties of the neuronal calcium sensor proteins VILIP-1 and VILIP-3: from subcellular localization to cellular function.	Spilker C, etal., Biochim Biophys Acta 2002 Nov 4;1600(1-2):118-27.

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	39,757,721 - 39,878,556 (-)	NCBI		GRCr8
mRatBN7.2	6	34,038,641 - 34,159,479 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	34,038,642 - 34,159,479 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	34,331,181 - 34,454,334 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	34,647,122 - 34,770,275 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	34,117,901 - 34,242,539 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	37,001,360 - 37,121,969 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	37,001,356 - 37,122,023 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	46,751,473 - 46,872,211 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	34,770,053 - 34,895,220 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	34,773,006 - 34,898,173 (-)	NCBI
Celera	6	33,439,096 - 33,557,484 (-)	NCBI		Celera
Cytogenetic Map	6	q15	NCBI

VSNL1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	17,539,972 - 17,657,018 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	17,539,126 - 17,657,018 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	17,721,239 - 17,838,285 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	17,585,288 - 17,701,187 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	17,643,597 - 17,759,331	NCBI
Celera	2	17,601,622 - 17,717,516 (+)	NCBI		Celera
Cytogenetic Map	2	p24.2	NCBI
HuRef	2	17,496,887 - 17,612,808 (+)	NCBI		HuRef
CHM1_1	2	17,651,208 - 17,767,107 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	17,571,738 - 17,688,768 (+)	NCBI		T2T-CHM13v2.0

Vsnl1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	11,375,258 - 11,486,579 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	11,375,243 - 11,486,614 (-)	Ensembl		GRCm39 Ensembl
GRCm38	12	11,325,257 - 11,436,578 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	11,325,242 - 11,436,613 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	11,332,051 - 11,443,455 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	11,351,590 - 11,462,956 (-)	NCBI		MGSCv36	mm8
Celera	12	11,670,526 - 11,784,645 (-)	NCBI		Celera
Cytogenetic Map	12	A1.1	NCBI
cM Map	12	5.58	NCBI

Vsnl1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955469	350,983 - 454,264 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955469	350,983 - 454,264 (+)	NCBI	ChiLan1.0	ChiLan1.0

VSNL1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	12	108,870,045 - 108,985,583 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	108,874,011 - 108,989,546 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	17,525,561 - 17,641,277 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	17,651,535 - 17,767,274 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	17,703,086 - 17,767,274 (+)	Ensembl	panpan1.1		panPan2

VSNL1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	17	13,022,232 - 13,109,590 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	17	12,974,424 - 13,077,644 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	17	13,158,446 - 13,261,846 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	17	13,158,459 - 13,261,844 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	17	13,017,163 - 13,120,174 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	17	13,028,296 - 13,131,379 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	17	13,054,319 - 13,157,641 (+)	NCBI		UU_Cfam_GSD_1.0

Vsnl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024406292	57,477,521 - 57,581,177 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936493	13,258,221 - 13,362,499 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936493	13,258,420 - 13,362,190 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

VSNL1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	120,177,895 - 120,288,143 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	120,177,897 - 120,288,157 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	128,325,755 - 128,436,018 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

VSNL1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	14	90,012,733 - 90,127,994 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	90,010,913 - 90,126,934 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	22,087,260 - 22,201,457 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Vsnl1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624738	512,835 - 611,190 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624738	511,977 - 611,190 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Vsnl1
619 total Variants

miRNA Target Status

Confirmed Target Of

miRNA Gene	Mature miRNA	Method Name	Result Type	Data Type	Support Type	PMID
Mir25	rno-miR-25-3p	Mirtarbase	external_info	Microarray	Functional MTI (Weak)	18258830
Mir494	rno-miR-494-3p	Mirtarbase	external_info	Microarray	Functional MTI (Weak)	18258830
Mir374b	rno-miR-374-5p	Mirtarbase	external_info	Microarray	Functional MTI (Weak)	18258830
Mir92a1	rno-miR-92a-3p	Mirtarbase	external_info	Microarray	Functional MTI (Weak)	18258830
Mir290	rno-miR-290	Mirtarbase	external_info	Microarray	Functional 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.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
8552962	Pigfal16	Plasma insulin-like growth factor 1 level QTL 16	9.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	1	41223769	Rat
634318	Bw118	Body weight QTL 118	3.55		abdominal fat pad mass (VT:1000711)	abdominal fat pad weight (CMO:0000088)	6	33309549	57730294	Rat
10401812	Kidm54	Kidney mass QTL 54			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	14368788	59368788	Rat
1331743	Uae28	Urinary albumin excretion QTL 28	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	1	34235784	Rat
2292589	Emca10	Estrogen-induced mammary cancer QTL 10		0.048	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	6	16536140	61536140	Rat
10401800	Kidm49	Kidney mass QTL 49			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	14368788	59368788	Rat
1300164	Rf15	Renal function QTL 15	3.12		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	5074497	54641141	Rat
1331779	Rf38	Renal function QTL 38	2.876		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	32074428	72227641	Rat
9589129	Insul24	Insulin level QTL 24	19.06	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	6	1	41223769	Rat
1578758	Tcas9	Tongue tumor susceptibility QTL 9	3.29		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	6	1	37618905	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	10894415	110548006	Rat
7411603	Foco13	Food consumption QTL 13	5.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	41223769	Rat
1598843	Cm63	Cardiac mass QTL 63	2.6		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	1	39036266	Rat
738024	Sach5	Saccharine consumption QTL 5	3.9	0.00039	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	6	1	43394190	Rat
7411542	Bw127	Body weight QTL 127	5.5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	1	41223769	Rat
9589048	Scfw3	Subcutaneous fat weight QTL 3	4.57	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	6	1	41223769	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	20866422	81133036	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	15107216	107351382	Rat
2293709	Bss23	Bone structure and strength QTL 23	5.18	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	6	1	42487980	Rat
2293650	Bss31	Bone structure and strength QTL 31	5.05	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	6	1	42487980	Rat
7411584	Foco4	Food consumption QTL 4	4.3	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	42838846	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	11735669	72593685	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	20866422	81133036	Rat
1300128	Rf16	Renal function QTL 16	3.89		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	5074497	34434305	Rat
1641898	Colcr4	Colorectal carcinoma resistance QTL4	3.71	0.0007	intestine integrity trait (VT:0010554)	well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)	6	20338777	62613667	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	11735669	72593685	Rat
6893340	Cm77	Cardiac mass QTL 77	0.26	0.57	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	33309549	81132889	Rat
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	72227641	Rat
2293656	Bss28	Bone structure and strength QTL 28	6.79	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	6	1	42487980	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	16536140	71636405	Rat

Markers in Region

D6Arb7

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	34,039,550 - 34,039,769 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	37,002,270 - 37,002,488	NCBI	Rnor6.0
Rnor_5.0	6	46,752,383 - 46,752,601	UniSTS	Rnor5.0
RGSC_v3.4	6	34,770,962 - 34,771,181	RGD	RGSC3.4
RGSC_v3.4	6	34,770,963 - 34,771,181	UniSTS	RGSC3.4
RGSC_v3.1	6	34,773,915 - 34,774,134	RGD
Celera	6	33,440,006 - 33,440,224	UniSTS
SHRSP x BN Map	6	28.5599	UniSTS
SHRSP x BN Map	6	28.5599	RGD
FHH x ACI Map	6	29.35	RGD
Cytogenetic Map	6	q14	UniSTS

D6Rat38

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	34,039,518 - 34,039,669 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	37,002,238 - 37,002,388	NCBI	Rnor6.0
Rnor_5.0	6	46,752,351 - 46,752,501	UniSTS	Rnor5.0
RGSC_v3.4	6	34,770,930 - 34,771,081	RGD	RGSC3.4
RGSC_v3.4	6	34,770,931 - 34,771,081	UniSTS	RGSC3.4
RGSC_v3.1	6	34,773,841 - 34,774,159	RGD
Celera	6	33,439,974 - 33,440,124	UniSTS
SHRSP x BN Map	6	28.5599	RGD
SHRSP x BN Map	6	28.5599	UniSTS
Cytogenetic Map	6	q14	UniSTS

D6Arb5

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	34,112,867 - 34,113,027 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	37,074,454 - 37,074,613	NCBI	Rnor6.0
Rnor_5.0	6	46,824,567 - 46,824,726	UniSTS	Rnor5.0
RGSC_v3.4	6	34,845,300 - 34,845,460	RGD	RGSC3.4
RGSC_v3.4	6	34,845,301 - 34,845,460	UniSTS	RGSC3.4
RGSC_v3.1	6	34,848,254 - 34,848,413	RGD
Celera	6	33,511,097 - 33,511,256	UniSTS
RH 3.4 Map	6	143.6	UniSTS
RH 3.4 Map	6	143.6	RGD
RH 2.0 Map	6	296.4	RGD
SHRSP x BN Map	6	28.4898	RGD
FHH x ACI Map	6	29.28	RGD
Cytogenetic Map	6	q14	UniSTS

D6Got35

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	34,073,680 - 34,073,812 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	37,036,397 - 37,036,528	NCBI	Rnor6.0
Rnor_5.0	6	46,786,510 - 46,786,641	UniSTS	Rnor5.0
RGSC_v3.4	6	34,806,092 - 34,806,224	RGD	RGSC3.4
RGSC_v3.4	6	34,806,093 - 34,806,224	UniSTS	RGSC3.4
RGSC_v3.1	6	34,809,046 - 34,809,177	RGD
Celera	6	33,474,053 - 33,474,184	UniSTS
RH 3.4 Map	6	142.3	RGD
RH 3.4 Map	6	142.3	UniSTS
Cytogenetic Map	6	q14	UniSTS

RH139543

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	34,038,959 - 34,039,172 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	37,001,679 - 37,001,891	NCBI	Rnor6.0
Rnor_5.0	6	46,751,792 - 46,752,004	UniSTS	Rnor5.0
RGSC_v3.4	6	34,770,372 - 34,770,584	UniSTS	RGSC3.4
Celera	6	33,439,415 - 33,439,627	UniSTS
RH 3.4 Map	6	145.8	UniSTS
Cytogenetic Map	6	q14	UniSTS

RH140383

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	34,038,795 - 34,038,996 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	37,001,515 - 37,001,715	NCBI	Rnor6.0
Rnor_5.0	6	46,751,628 - 46,751,828	UniSTS	Rnor5.0
RGSC_v3.4	6	34,770,208 - 34,770,408	UniSTS	RGSC3.4
Celera	6	33,439,251 - 33,439,451	UniSTS
Cytogenetic Map	6	q14	UniSTS

RH80046

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	34,038,933 - 34,039,121 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	37,001,653 - 37,001,840	NCBI	Rnor6.0
Rnor_5.0	6	46,751,766 - 46,751,953	UniSTS	Rnor5.0
RGSC_v3.4	6	34,770,346 - 34,770,533	UniSTS	RGSC3.4
Celera	6	33,439,389 - 33,439,576	UniSTS
Cytogenetic Map	6	q14	UniSTS

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		54	38						192		3	36
Low	16	80	102	60	51	60	36	36	40	72	109	21	24
Below cutoff	5	7	46	46	18	46		9	18	43	30

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_012686	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	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
	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000007609 ⟹ ENSRNOP00000007609

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	34,038,642 - 34,159,479 (-)	Ensembl
Rnor_6.0 Ensembl	6	37,001,356 - 37,122,023 (-)	Ensembl

RefSeq Acc Id:

NM_012686 ⟹ NP_036818

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	39,757,721 - 39,878,556 (-)	NCBI
mRatBN7.2	6	34,038,641 - 34,159,479 (-)	NCBI
Rnor_6.0	6	37,001,360 - 37,121,969 (-)	NCBI
Rnor_5.0	6	46,751,473 - 46,872,211 (-)	NCBI
RGSC_v3.4	6	34,770,053 - 34,895,220 (-)	RGD
Celera	6	33,439,096 - 33,557,484 (-)	RGD

Sequence:

show sequence

CCCAATCTGCAGCAGAGATTCACCCGAGCGTGTTGCAGCGGCCACTGGGCTTGCAAGGCGCAAT
CCAAGAGGGATTTAAGCAGCCCGGAGCTCCCAGAAAAGAAGCGAGAGAGAACCACTCACAGAGA
CGGTTTAGCCGTTAGTCTGAATTAAATATATATATTTTTTTGAAAGAACTGTTTAGTTTTATCA
TTTTCCTTAAGTGACGGTGCACAGCGCTATAACTGCAAAATGGGGAAACAGAATAGCAAACTGG
CCCCAGAAGTCATGGAGGACCTGGTGAAGAGCACCGAGTTCAATGAGCATGAGCTCAAGCAGTG
GTACAAGGGCTTCCTCAAGGACTGTCCGAGCGGGAGGCTGAATCTCGAAGAGTTCCAGCAGCTC
TATGTGAAGTTCTTCCCCTATGGAGATGCCTCCAAGTTCGCTCAGCACGCCTTCCGCACCTTCG
ACAAGAATGGTGATGGCACCATCGACTTCCGAGAGTTCATCTGTGCTCTGTCCATCACCTCCAG
AGGCAGCTTTGAGCAGAAACTGAACTGGGTTTTCAACATGTATGATCTGGATGGTGACGGCAAG
ATCACCAGGGTGGAGATGCTGGAGATTATCGAGGCTATCTACAAGATGGTGGGCACTGTGATCA
TGATGAAAATGAATGAGGATGGCCTCACGCCAGAACAGCGAGTGGACAAGATTTTCAGCAAGAT
GGATAAGAACAAAGATGACCAGATTACATTGGATGAATTCAAAGAAGCTGCAAAAAGCGACCCT
TCCATTGTATTACTCCTGCAGTGCGACATTCAGAAATGAGCTGATGTCAATGCTATGGACTGCA
CAGAAGTCTTGATGTTCCATTCAGTCTGCAGCTACACACACACACACACACACACACACACACA
CACACACACACTACACACACACACAATTGCTTGGACTACCTATAAATGGACTTGCTTCTTGTGT
TTGAAACACTTGTGTGCATGAGAATGTCATTTGCTAATGAATTTTAAAAGCATATATTATAAAA
ACCCAACAACCGGCCACAATGTGATATGTGTAATATCATTTCATCAAATTACATCTTCCTCCAA
AGCCTGGGCAGAAGCGTGCTGCAAAGAATTCTATGATTTCTTGTACATGTTTTGCTAATGCTTG
TGTCTCCTTGATTATATAATATTAGTAGCACTGAGACCCCCCACGGTAATGTAACTTATTATGG
GCTGCGTCACCATTCTCCTGTAAAATAGTACTGGACAGACACAGGAGGGGCCCTTGGCTTCCTG
TCTGGCCCACATACAATACACAGCTTGTATTATCAGTGAATATAAATGTACTACATTTGCATGC
CTTTGGGTTTGCCTTAATTCTTACCTCATTTGTAACCTCTCGATCTGGAAAGAGCTGTTTTGGA
TGAATGCAGTATACAACTTAAAAATCCTGCTAAACTATTCATTAAGTATAACTATCTATATATC
TATAGACACAAAGGTATTATATATTGAACATAAAAACATAATAATGGGAATGTATTGATTTGTT
TGACGTTTCAGAGGCTTCCAGAAAGGTGGCAATAGATGTCCCAAATAAATTTCTAATATTTGAT
TTAGTCCCCTAATTATTAATTTACCATTTTCAGCTCAATGTTCATAGGGGTCAGCTAGTGATGA
CTTACTAAATCTACCCTTACACACATCTTTGGAATTTGCAGAATGACTGAAGGGGGGGGGGGAA
GGAAAGTCACTTTCCAACTTGTCATCCAGCCCCTCCCCCAAAGAGGGCTAATTAATATGGCATG
TAACATTTAAAGAAAACAGGAGATTTGTTCATTCTGGAAAACAATGCTCATTATGTGACAATAA
ACTTTATCTCAGTGTGAAAAAAAAAAAAAAAAAAAAAAA

hide 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
Ensembl Protein	ENSRNOP00000007609.3
	ENSRNOP00055006872
	ENSRNOP00060004689
	ENSRNOP00065005589
GenBank Protein	P62762	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_036818 ⟸ NM_012686
- UniProtKB:	Q56A29 (UniProtKB/TrEMBL)
- Sequence:	show sequence MGKQNSKLAPEVMEDLVKSTEFNEHELKQWYKGFLKDCPSGRLNLEEFQQLYVKFFPYGDASKF AQHAFRTFDKNGDGTIDFREFICALSITSRGSFEQKLNWVFNMYDLDGDGKITRVEMLEIIEAI YKMVGTVIMMKMNEDGLTPEQRVDKIFSKMDKNKDDQITLDEFKEAAKSDPSIVLLLQCDIQK hide sequence

Ensembl Acc Id:

ENSRNOP00000007609 ⟸ ENSRNOT00000007609

Protein Domains

EF-hand

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P62762-F1-model_v2	AlphaFold	P62762	1-191	view protein structure

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	37,121,966 - 37,122,026	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3966	AgrOrtholog
BioCyc Gene	G2FUF-38142	BioCyc
Ensembl Genes	ENSRNOG00000005345	Ensembl, UniProtKB/Swiss-Prot
	ENSRNOG00055005616	UniProtKB/Swiss-Prot
	ENSRNOG00060003772	UniProtKB/Swiss-Prot
	ENSRNOG00065005407	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000007609.6	UniProtKB/Swiss-Prot
	ENSRNOT00055009028	UniProtKB/Swiss-Prot
	ENSRNOT00060006285	UniProtKB/Swiss-Prot
	ENSRNOT00065008002	UniProtKB/Swiss-Prot
Gene3D-CATH	EF-hand	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
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
PRINTS	RECOVERIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	EF_HAND_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_HAND_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000005345	RatGTEx
	ENSRNOG00055005616	RatGTEx
	ENSRNOG00060003772	RatGTEx
	ENSRNOG00065005407	RatGTEx
SMART	EFh	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF47473	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A6HAP8_RAT	UniProtKB/TrEMBL
	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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - CTD