Isl1 (ISL LIM homeobox 1) - Rat Genome Database

Name: Isl1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Isl1 (ISL LIM homeobox 1) Rattus norvegicus

Analyze

Symbol:

Isl1

Name:

ISL LIM homeobox 1

RGD ID:

61957

Description:

Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and nuclear estrogen receptor binding activity. Involved in several processes, including cellular response to glucocorticoid stimulus; negative regulation of intracellular estrogen receptor signaling pathway; and positive regulation of insulin secretion. Located in nucleus. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus and type 2 diabetes mellitus. Orthologous to human ISL1 (ISL LIM homeobox 1); INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; all-trans-retinoic acid; ammonium chloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

ISL1 transcription factor, LIM/homeodomain, (islet-1) ; insulin gene enhancer protein ISL-1; Isl-1; isl-1 homeobox; isl-1=homeobox; ISL1 transcription factor LIM/homeodomain; ISL1 transcription factor LIM/homeodomain (islet-1); ISL1 transcription factor, LIM/homeodomain; ISL1 transcription factor, LIM/homeodomain 1; islet-1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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):	ISL1 (ISL LIM homeobox 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Isl1 (ISL1 transcription factor, LIM/homeodomain)	HGNC	Treefam, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Isl1 (ISL LIM homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ISL1 (ISL LIM homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ISL1 (ISL LIM homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Isl1 (ISL LIM homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ISL1 (ISL LIM homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ISL1 (ISL LIM homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Isl1 (ISL LIM homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	ISL2 (ISL LIM homeobox 2)	HGNC	OrthoDB
Alliance orthologs ³
Mus musculus (house mouse):	Isl1 (ISL1 transcription factor, LIM/homeodomain)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Homo sapiens (human):	ISL1 (ISL LIM homeobox 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Danio rerio (zebrafish):	isl1 (ISL LIM homeobox 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Caenorhabditis elegans (roundworm):	lim-7	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Drosophila melanogaster (fruit fly):	tup	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)

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
mRatBN7.2	2	48,079,412 - 48,090,704 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	2	48,080,522 - 48,095,584 (-)	Ensembl
Rnor_6.0	2	48,488,911 - 48,501,217 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	48,487,736 - 48,501,436 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	66,871,790 - 66,883,936 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	48,050,124 - 48,060,394 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	47,978,356 - 47,988,627 (-)	NCBI
Celera	2	43,808,350 - 43,818,250 (-)	NCBI		Celera
Cytogenetic Map	2	q14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

bladder exstrophy-epispadias-cloacal exstrophy complex (ISO)

congenital heart disease (ISO)

Neoplasm Recurrence, Local (ISO)

neuroblastoma (ISO)

Neurodevelopmental Disorders (ISO)

type 1 diabetes mellitus (ISO)

type 2 diabetes mellitus (ISO)

urinary bladder cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2-methylcholine (ISO)

3,3',4,4',5-pentachlorobiphenyl (EXP)

3-Nitrobenzanthrone (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-fluorouracil (ISO)

acetic acid (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (EXP,ISO)

ammonium chloride (EXP)

antimycin A (ISO)

arachidonic acid (ISO)

arotinoid acid (ISO)

arsane (ISO)

arsenic atom (ISO)

benzalkonium chloride (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

carbamazepine (ISO)

CHIR 99021 (ISO)

cortisol (ISO)

cyclosporin A (ISO)

DDE (EXP)

dexamethasone (EXP)

dorsomorphin (ISO)

ethanol (ISO)

folic acid (ISO)

fulvestrant (ISO)

homocysteine (ISO)

inositol (ISO)

L-ascorbic acid (ISO)

L-ascorbic acid 2-phosphate (ISO)

mercury dibromide (ISO)

methylmercury chloride (ISO)

Muraglitazar (EXP)

N-methyl-4-phenylpyridinium (ISO)

panobinostat (ISO)

phenylmercury acetate (ISO)

pioglitazone (ISO)

ribavirin (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

tebufenpyrad (ISO)

thifluzamide (ISO)

triacsin C (ISO)

trichloroethene (EXP)

trichostatin A (ISO)

triclosan (ISO)

troglitazone (EXP)

valproic acid (ISO)

vorinostat (ISO)

XAV939 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

atrial septum morphogenesis (ISO)

axon regeneration (IEP)

axonogenesis (IBA)

canonical Wnt signaling pathway (IEA,ISO)

cardiac cell fate determination (ISO)

cardiac muscle cell myoblast differentiation (ISO)

cardiac right ventricle morphogenesis (ISO)

cell population proliferation (IEA,ISO)

cellular response to glucocorticoid stimulus (IEP)

endocardial cushion morphogenesis (ISO)

heart development (ISO,ISS)

heart morphogenesis (ISO)

innervation (ISO)

mesenchymal cell differentiation (ISO)

negative regulation of canonical Wnt signaling pathway (ISO)

negative regulation of epithelial cell proliferation (IMP)

negative regulation of inflammatory response (ISO)

negative regulation of intracellular estrogen receptor signaling pathway (IDA)

negative regulation of neuron apoptotic process (ISO)

negative regulation of neuron differentiation (ISO)

negative regulation of protein-containing complex assembly (IDA)

negative regulation of transcription by RNA polymerase II (ISO)

neural crest cell migration (ISO)

neuron differentiation (ISO)

neuron fate commitment (ISO)

neuron fate specification (IBA,ISO)

outflow tract morphogenesis (ISO)

outflow tract septum morphogenesis (ISO)

pancreas development (ISO)

peripheral nervous system neuron axonogenesis (ISO)

peripheral nervous system neuron development (ISO)

pharyngeal system development (ISO)

pituitary gland development (ISO)

positive regulation of angiogenesis (ISO)

positive regulation of cell differentiation (ISO,ISS)

positive regulation of cell population proliferation (ISO)

positive regulation of DNA binding (ISO)

positive regulation of epithelial to mesenchymal transition (IMP)

positive regulation of granulocyte colony-stimulating factor production (ISO)

positive regulation of granulocyte macrophage colony-stimulating factor production (ISO)

positive regulation of histone acetylation (ISO)

positive regulation of insulin secretion (IMP)

positive regulation of interferon-gamma production (ISO)

positive regulation of interleukin-1 alpha production (ISO)

positive regulation of interleukin-1 beta production (ISO)

positive regulation of interleukin-12 production (ISO)

positive regulation of interleukin-6 production (ISO)

positive regulation of macrophage colony-stimulating factor production (ISO)

positive regulation of transcription by RNA polymerase II (IBA,IDA,ISO)

positive regulation of tumor necrosis factor production (ISO)

positive regulation of tyrosine phosphorylation of STAT protein (ISO)

positive regulation of vascular endothelial growth factor production (ISO)

regulation of gene expression (ISO)

regulation of heart rate by cardiac conduction (ISO)

regulation of secondary heart field cardioblast proliferation (ISO)

regulation of transcription by RNA polymerase II (IBA)

regulation of transcription, DNA-templated (IDA)

retinal ganglion cell axon guidance (ISO)

secondary heart field specification (ISO)

sensory system development (ISO)

sinoatrial node cell development (ISO)

spinal cord motor neuron cell fate specification (ISO)

spinal cord motor neuron differentiation (ISO)

stem cell differentiation (ISO)

transcription by RNA polymerase II (IEA,ISO)

trigeminal nerve development (ISO)

ventricular cardiac muscle tissue morphogenesis (ISO)

visceral motor neuron differentiation (ISO)

Cellular Component

nucleus (IBA,IDA,ISO)

Molecular Function

bHLH transcription factor binding (ISO)

chromatin binding (ISO)

cis-regulatory region sequence-specific DNA binding (IBA,ISO)

DNA binding (ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (IDA,ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA,ISO)

metal ion binding (IEA)

nuclear estrogen receptor binding (IDA)

nuclear receptor binding (IDA,IPI)

promoter-specific chromatin binding (ISO,ISS)

protein binding (IPI,ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IDA)

RNA polymerase II-specific DNA-binding transcription factor binding (ISO)

sequence-specific DNA binding (IDA,ISO)

sequence-specific double-stranded DNA binding (ISO)

References

References - curated


1.	Barat-Houari M, etal., Diabetes. 2002 May;51(5):1640-3.
2.	Behravan G, etal., Protein Eng. 1997 Nov;10(11):1327-31.
3.	Brønnum H, etal., Exp Cell Res. 2013 Feb 15;319(4):424-35. doi: 10.1016/j.yexcr.2012.12.019. Epub 2012 Dec 24.
4.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	Gay F, etal., Mol Endocrinol. 2000 Oct;14(10):1627-48.
6.	Granger A, etal., Mol Endocrinol. 2006 Sep;20(9):2093-108. Epub 2006 Apr 13.
7.	Hol EM, etal., Neuroscience. 1999;88(3):917-25.
8.	Holm P, etal., Diabetes. 2004 Jun;53(6):1584-91.
9.	Jurata LW and Gill GN, Mol Cell Biol. 1997 Oct;17(10):5688-98.
10.	Karlsson O, etal., Nature 1990 Apr 26;344(6269):879-82.
11.	Kojima H, etal., Diabetes 2002 May;51(5):1398-408.
12.	MGD data from the GO Consortium
13.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
14.	RGD automated import pipeline for gene-chemical interactions
15.	Wang M and Drucker DJ, Endocrinology 1994 Mar;134(3):1416-22.
16.	Wang M and Drucker DJ, J Biol Chem. 1995 May 26;270(21):12646-52.
17.	Zhang H, etal., J Mol Biol. 2009 Sep 25;392(3):566-77. doi: 10.1016/j.jmb.2009.07.036. Epub 2009 Jul 17.

Additional References at PubMed

PMID:8565076	PMID:9000074	PMID:9806931	PMID:10536059	PMID:12900460	PMID:14664703	PMID:14667410	PMID:14702043	PMID:14766174	PMID:15659653	PMID:16321656	PMID:16687132
PMID:17519333	PMID:17553340	PMID:17928203	PMID:18367596	PMID:18434416	PMID:18434421	PMID:18524626	PMID:18849985	PMID:19571884	PMID:19620969	PMID:19666821	PMID:20520780
PMID:21734270	PMID:22343290	PMID:22343712	PMID:22727192	PMID:23610558	PMID:23805044	PMID:24147056	PMID:24310985	PMID:24643061	PMID:24821700	PMID:25433207	PMID:25775587
PMID:26393440

Genomics

Comparative Map Data

Isl1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	2	48,079,412 - 48,090,704 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	2	48,080,522 - 48,095,584 (-)	Ensembl
Rnor_6.0	2	48,488,911 - 48,501,217 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	48,487,736 - 48,501,436 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	66,871,790 - 66,883,936 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	48,050,124 - 48,060,394 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	47,978,356 - 47,988,627 (-)	NCBI
Celera	2	43,808,350 - 43,818,250 (-)	NCBI		Celera
Cytogenetic Map	2	q14	NCBI

ISL1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	51,383,448 - 51,394,730 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	5	51,383,448 - 51,394,730 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	5	50,679,282 - 50,690,564 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	50,714,715 - 50,726,321 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	50,715,025 - 50,726,310	NCBI
Celera	5	47,625,609 - 47,637,216 (+)	NCBI
Cytogenetic Map	5	q11.1	NCBI
HuRef	5	47,642,569 - 47,654,183 (+)	NCBI		HuRef
CHM1_1	5	50,681,961 - 50,693,557 (+)	NCBI		CHM1_1

Isl1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	116,434,806 - 116,446,224 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	13	116,434,817 - 116,446,225 (-)	Ensembl
GRCm38	13	116,298,270 - 116,309,688 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	116,298,281 - 116,309,689 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	117,088,478 - 117,099,896 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	13	117,418,963 - 117,430,370 (-)	NCBI			mm8
Celera	13	120,696,034 - 120,707,388 (-)	NCBI		Celera
Cytogenetic Map	13	D2.2	NCBI

Isl1
(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_004955446	15,824,035 - 15,835,046 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955446	15,824,956 - 15,835,000 (-)	NCBI	ChiLan1.0	ChiLan1.0

ISL1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	5	64,253,037 - 64,264,674 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	64,252,715 - 64,264,674 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	62,635,095 - 62,650,141 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

ISL1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	4	63,638,009 - 63,648,492 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	4	63,637,443 - 63,648,183 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	4	63,397,586 - 63,408,606 (-)	NCBI
ROS_Cfam_1.0	4	64,141,344 - 64,152,383 (-)	NCBI
ROS_Cfam_1.0 Ensembl	4	64,141,331 - 64,152,087 (-)	Ensembl
UMICH_Zoey_3.1	4	63,906,232 - 63,917,266 (-)	NCBI
UNSW_CanFamBas_1.0	4	64,028,384 - 64,039,422 (-)	NCBI
UU_Cfam_GSD_1.0	4	64,567,747 - 64,578,778 (-)	NCBI

Isl1
(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_024407213	206,869,998 - 206,881,359 (-)	NCBI
SpeTri2.0	NW_004936480	15,805,259 - 15,817,854 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ISL1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	16	30,963,000 - 30,973,907 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	16	30,962,994 - 30,974,201 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	16	32,548,015 - 32,559,227 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ISL1
(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	4	47,665,861 - 47,678,631 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	4	47,666,536 - 47,677,552 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666082	3,504,978 - 3,526,896 (-)	NCBI	Vero_WHO_p1.0

Isl1
(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 1.0	NW_004624759	7,996,177 - 8,006,281 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

PMC186328P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	48,086,133 - 48,086,320 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	48,494,429 - 48,494,615	NCBI	Rnor6.0
Rnor_5.0	2	66,877,308 - 66,877,494	UniSTS	Rnor5.0
RGSC_v3.4	2	48,055,642 - 48,055,828	UniSTS	RGSC3.4
Celera	2	43,813,868 - 43,814,054	UniSTS
Cytogenetic Map	2	q15	UniSTS

RH141578

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	48,082,313 - 48,082,512 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	48,490,609 - 48,490,807	NCBI	Rnor6.0
Rnor_5.0	2	66,873,488 - 66,873,686	UniSTS	Rnor5.0
RGSC_v3.4	2	48,051,822 - 48,052,020	UniSTS	RGSC3.4
Celera	2	43,810,048 - 43,810,246	UniSTS
RH 3.4 Map	2	327.7	UniSTS
Cytogenetic Map	2	q15	UniSTS

D10Bir8

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_5.0	4	66,216,096 - 66,216,306	NCBI	Rnor5.0
Rnor_5.0	10	102,852,602 - 102,852,872	NCBI	Rnor5.0
RGSC_v3.4	10	104,539,788 - 104,540,057	UniSTS	RGSC3.4
RGSC_v3.4	4	66,232,144 - 66,232,353	UniSTS	RGSC3.4
Celera	10	98,286,975 - 98,287,244	UniSTS
Celera	4	62,414,402 - 62,414,611	UniSTS
Cytogenetic Map	10	q32.2	UniSTS
Cytogenetic Map	2	q15	UniSTS

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
2293835	Kiddil5	Kidney dilation QTL 5	3.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	157142209	Rat
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	182042367	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	2	40067944	102785628	Rat
631208	Bw1	Body weight QTL1	5.09		mesenteric fat pad mass (VT:0010427)	mesenteric fat pad weight to body weight ratio (CMO:0000654)	2	43171017	83575226	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46123260	202447032	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43154682	202446871	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43154682	202446871	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
731167	Glom4	Glomerulus QTL 4	2.4	0.0082	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	2	20304672	65304672	Rat
731184	Mamtr4	Mammary tumor resistance QTL 4		0.0003	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	2	16491740	61491740	Rat
738012	Anxrr3	Anxiety related response QTL 3	3.8		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	2	9023519	54023519	Rat
1300155	Bp174	Blood pressure QTL 174	4.09		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	2	42804607	60653831	Rat
1302794	Stl27	Serum triglyceride level QTL 27	4.4	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	2	25413423	143657569	Rat
1643006	Pain1	Pain QTL 1	3.63	0.005	mechanical nociception trait (VT:0002734)	self mutilation severity score (CMO:0002145)	2	26999571	48268661	Rat
2300168	Bmd47	Bone mineral density QTL 47	6.6	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	2	20662448	65662448	Rat
2293671	Bss44	Bone structure and strength QTL 44	10.97	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	2	43162366	148478373	Rat
2293676	Bmd19	Bone mineral density QTL 19	10.7	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	2	43162366	111362592	Rat
2293682	Bmd24	Bone mineral density QTL 24	8.9	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	2	43162366	111362592	Rat
1578664	Bmd9	Bone mineral QTL density 9	5		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	2	11852062	49003364	Rat
1300160	Hrtrt3	Heart rate QTL 3	3.62		heart pumping trait (VT:2000009)	absolute change in heart rate (CMO:0000534)	2	29971593	51729300	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43171017	184114403	Rat
1354603	Bp243	Blood pressure QTL 243	3.9		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26917817	127469484	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	26917817	81754745	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	26917817	81754745	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26917817	81754745	Rat
1357990	Ael1	Aortic elastin QTL 1	3.1	0.00091	aorta elastin amount (VT:0003905)	aortic elastin	2	19076825	64076825	Rat
2290453	Scl55	Serum cholesterol level QTL 55	2.83		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	2	26917817	136917119	Rat
1358887	Bw50	Body weight QTL 50	2.39		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1358894	Kidm24	Kidney mass QTL 24	4.03		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358899	Kidm23	Kidney mass QTL 23	3.88		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358901	Cm38	Cardiac mass QTL 38	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358904	Cm39	Cardiac mass QTL 39	2.26		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358908	Bw49	Body weight QTL 49	3.36		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1358910	Kidm27	Kidney mass QTL 27	5.77		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358911	Kidm28	Kidney mass QTL 28	5.42		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
61355	Bp36	Blood pressure QTL 36	2.9		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	2	5873687	102844969	Rat
61371	Edpm1	Estrogen-dependent pituitary mass QTL 1	4	0.05	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	35134841	88029593	Rat
9590095	Sffal3	Serum free fatty acids level QTL 3	6.78	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	2	27157160	72157160	Rat
10402051	Gdil2	Gastrointestinal dilation QTL 2			enteric ganglion morphology trait (VT:0001045)	length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)	2	24903853	74786777	Rat
10755436	Coatc8	Coat color QTL 8		0.02431	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	35023117	80023117	Rat
12879863	Bp402	Blood pressure QTL 402		0.003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	41125789	56532139	Rat
10755434	Coatc7	Coat color QTL 7		0.04794	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	30648065	75648065	Rat
10755430	Coatc6	Coat color QTL 6		0.02576	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	11591100	56591100	Rat

miRNA Target Status

Confirmed Target Of

miRNA Gene	Mature miRNA	Method Name	Result Type	Data Type	Support Type	PMID
Mir31	rno-miR-31a-5p	Mirtarbase	external_info	Immunofluorescence//Luciferase reporter assay	Functional MTI	23270756

Predicted Target Of

	Summary Value
Count of predictions:	40
Count of miRNA genes:	39
Interacting mature miRNAs:	39
Transcripts:	ENSRNOT00000017305
Prediction methods:	Microtar, 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			2	2		2			31		9
Low	1	20	20	4	8	4			32	4	19	9
Below cutoff	2	19	21	21	9	21	6	7	11	5	8	2	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017339	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039103065	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039103066	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AY557632	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473955	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000065	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	S69329	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000017305 ⟹ ENSRNOP00000017305

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	2	48,080,616 - 48,095,584 (-)	Ensembl
Rnor_6.0 Ensembl	2	48,487,736 - 48,501,436 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000117391 ⟹ ENSRNOP00000076523

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	2	48,080,522 - 48,090,444 (-)	Ensembl

RefSeq Acc Id:

NM_017339 ⟹ NP_059035

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	48,080,616 - 48,090,444 (-)	NCBI
Rnor_6.0	2	48,488,911 - 48,501,217 (-)	NCBI
Rnor_5.0	2	66,871,790 - 66,883,936 (-)	NCBI
RGSC_v3.4	2	48,050,124 - 48,060,394 (-)	RGD
Celera	2	43,808,350 - 43,818,250 (-)	RGD

Sequence:

show sequence

CAGATATGGGAGACATGGGCGATCCACCAAAAAAAAAACGTCTGATTTCCCTATGTGTTGGTTG
CGGTAATCAAATTCACGATCAGTATATTCTGAGGGTTTCTCCGGATTTGGAATGGCATGCGGCA
TGTTTGAAATGTGCGGAGTGTAATCAGTATTTGGACGAAAGCTGTACCTGCTTTGTTAGGGACG
GGAAAACCTACTGTAAAAGAGATTATATCAGGTTGTACGGGATCAAATGCGCCAAGTGCAGCAT
AGGCTTCAGCAAGAACGACTTCGTGATGCGCGCCCGCTCTAAGGTGTACCACATCGAATGTTTC
CGCTGTGTAGCATGCAGCCGACAGCTCATCCCGGGAGACGAATTCGCGCTGCGGGAGGATGGGC
TTTTCTGCCGCGCGGACCACGATGTAGTGGAGAGGGCCAGCCTAGGAGCTGGAGACCCTCTCAG
TCCCTTGCATCCAGCGCGGCCTCTGCAAATGGCAGCCGAGCCCATCTCCGCTAGGCAGCCAGCT
CTGCGGCCGCACGTCCACAAACAGCCCGAGAAGACCACCCGAGTGCGGACTGTGCTCAACGAAA
AGCAGCTGCACACCTTGCGGACCTGCTACGCAGCCAACCCTCGGCCAGATGCGCTCATGAAGGA
GCAACTAGTGGAGATGACCGGCCTCAGTCCCCGAGTCATCCGGGTCTGGTTTCAAAACAAGAGG
TGCAAGGACAAGAAACGCAGCATCATGATGAAGCAGCTCCAGCAGCAGCAACCCAACGACAAAA
CTAATATCCAGGGGATGACAGGAACTCCCATGGTGGCTGCTAGTCCGGAGAGACATGATGGTGG
TTTACAGGCTAACCCAGTTGAGGTGCAAAGTTACCAGCCGCCCTGGAAAGTACTGAGTGACTTC
GCCTTGCAAAGTGACATAGATCAGCCTGCTTTTCAGCAACTGGTCAATTTTTCAGAAGGAGGAC
CAGGCTCTAATTCCACTGGCAGTGAAGTAGCATCGATGTCCTCTCAGCTCCCAGATACACCCAA
CAGCATGGTAGCCAGTCCTATAGAGGCATGAGGAAC

hide sequence

RefSeq Acc Id:

XM_039103065 ⟹ XP_038958993

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	48,079,412 - 48,090,704 (-)	NCBI

RefSeq Acc Id:

XM_039103066 ⟹ XP_038958994

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	48,080,338 - 48,090,400 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_059035	(Get FASTA)	NCBI Sequence Viewer
	XP_038958993	(Get FASTA)	NCBI Sequence Viewer
	XP_038958994	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB30128	(Get FASTA)	NCBI Sequence Viewer
	AAS46773	(Get FASTA)	NCBI Sequence Viewer
	EDM10395	(Get FASTA)	NCBI Sequence Viewer
	P61374	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_059035 ⟸ NM_017339

- UniProtKB:

P61374 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MGDMGDPPKKKRLISLCVGCGNQIHDQYILRVSPDLEWHAACLKCAECNQYLDESCTCFVRDGK
TYCKRDYIRLYGIKCAKCSIGFSKNDFVMRARSKVYHIECFRCVACSRQLIPGDEFALREDGLF
CRADHDVVERASLGAGDPLSPLHPARPLQMAAEPISARQPALRPHVHKQPEKTTRVRTVLNEKQ
LHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIMMKQLQQQQPNDKTN
IQGMTGTPMVAASPERHDGGLQANPVEVQSYQPPWKVLSDFALQSDIDQPAFQQLVNFSEGGPG
SNSTGSEVASMSSQLPDTPNSMVASPIEA

hide sequence

RefSeq Acc Id:

ENSRNOP00000017305 ⟸ ENSRNOT00000017305

RefSeq Acc Id:	XP_038958993 ⟸ XM_039103065
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038958994 ⟸ XM_039103066
- Peptide Label:	isoform X2

RefSeq Acc Id:

ENSRNOP00000076523 ⟸ ENSRNOT00000117391

Protein Domains

LIM zinc-binding

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P61374-F1-model_v2	AlphaFold	P61374	1-349	view protein structure

Transcriptome

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

Strain Variation

Strain Sequence Variants (MRatBN7.2)

ACI/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN-Lx/CubMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BUF/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

DA/OlaHsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE16/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/FarMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB10/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF10A/StmMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/NRrrcMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MWF/Hsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHR/OlalpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WAG/RijCrl (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:61957	AgrOrtholog
BioCyc Gene	G2FUF-54311	BioCyc
Ensembl Genes	ENSRNOG00000012556	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000017305	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000076523	ENTREZGENE
Ensembl Transcript	ENSRNOT00000017305	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000117391	ENTREZGENE
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot
	Znf_LIM	UniProtKB/Swiss-Prot
KEGG Report	rno:64444	UniProtKB/Swiss-Prot
NCBI Gene	64444	ENTREZGENE
Pfam	Homeodomain	UniProtKB/Swiss-Prot
	LIM	UniProtKB/Swiss-Prot
PhenoGen	Isl1	PhenoGen
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot
	LIM_DOMAIN_1	UniProtKB/Swiss-Prot
	LIM_DOMAIN_2	UniProtKB/Swiss-Prot
SMART	HOX	UniProtKB/Swiss-Prot
	LIM	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot
UniProt	ISL1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	P20663	UniProtKB/Swiss-Prot
	P47894	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2009-02-26	Isl1	ISL LIM homeobox 1	Isl1	ISL1 transcription factor, LIM/homeodomain 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2003-04-09	Isl1	ISL1 transcription factor, LIM/homeodomain 1			Symbol and Name updated	629477	APPROVED
2003-03-12	Isl1	ISL1 transcription factor, LIM/homeodomain 1	Isl-1	isl-1=homeobox	Data Merged	628472	PROVISIONAL
2002-08-07	Isl-1	isl-1=homeobox			Symbol and Name status set to provisional	70820	PROVISIONAL
2002-06-10	Isl1	ISL1 transcription factor, LIM/homeodomain			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in central and peripheral nervous system and the islet cells of the pancreas	729019

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 - ClinVar

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