Lhx2 (LIM homeobox 2) - Rat Genome Database

Name: Lhx2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Lhx2 (LIM homeobox 2) Rattus norvegicus

Analyze

Symbol:

Lhx2

Name:

LIM homeobox 2

RGD ID:

71076

Description:

Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in neuron differentiation. Predicted to be active in nucleus. Orthologous to human LHX2 (LIM homeobox 2); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 3H-1,2-dithiole-3-thione; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

homeobox protein LH-2; Lh-2; LH2A; LIM homeobox protein 2; LIM/homeobox protein Lhx2; LOC296706

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):	LHX2 (LIM homeobox 2)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Lhx2 (LIM homeobox protein 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lhx2 (LIM homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LHX2 (LIM homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LHX2 (LIM homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lhx2 (LIM homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LHX2 (LIM homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LHX2 (LIM homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lhx2 (LIM homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	LHX2 (LIM homeobox 2)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Lhx2 (LIM homeobox protein 2)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	lhx2b (LIM homeobox 2b)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	ap	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ttx-3	Alliance	DIOPT (Hieranoid\|InParanoid\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	lhx2	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
mRatBN7.2	3	22,113,619 - 22,143,909 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	22,126,007 - 22,143,908 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	25,594,877 - 25,612,777 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	3	34,179,870 - 34,197,771 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	3	31,991,800 - 32,009,717 (+)	NCBI	Rnor_WKY
Rnor_6.0	3	22,628,674 - 22,658,447 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	22,640,545 - 22,658,446 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	27,870,008 - 27,887,929 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	18,129,455 - 18,147,357 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	18,025,179 - 18,043,730 (+)	NCBI
Celera	3	20,559,471 - 20,577,366 (+)	NCBI		Celera
Cytogenetic Map	3	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

rheumatoid arthritis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-colchicine (ISO)

14-Deoxy-11,12-didehydroandrographolide (ISO)

2,2',5,5'-tetrachlorobiphenyl (EXP)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

3H-1,2-dithiole-3-thione (EXP)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

adenine (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

amosite asbestos (ISO)

arsenite(3-) (ISO)

azoxystrobin (EXP)

belinostat (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

cadmium dichloride (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chlorpyrifos (EXP)

cisplatin (ISO)

copper(II) sulfate (ISO)

coumestrol (ISO)

crocidolite asbestos (ISO)

cyclophosphamide (EXP)

dexamethasone (EXP)

diclofenac (ISO)

dorsomorphin (ISO)

entinostat (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

etoposide (ISO)

flusilazole (ISO)

fulvestrant (ISO)

glyphosate (EXP)

hydroxyurea (ISO)

imidacloprid (EXP)

lipopolysaccharide (ISO)

mercury dibromide (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

mitomycin C (ISO)

Monobutylphthalate (EXP)

N-ethyl-N-nitrosourea (EXP)

N-nitrosodiethylamine (ISO)

nickel sulfate (ISO)

p-chloromercuribenzoic acid (ISO)

panobinostat (ISO)

paracetamol (EXP,ISO)

PCB138 (EXP)

pentanal (ISO)

phenobarbital (ISO)

phenylmercury acetate (ISO)

resveratrol (ISO)

rotenone (ISO)

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

SB 431542 (ISO)

serpentine asbestos (ISO)

silicon dioxide (ISO)

sodium dichromate (EXP)

succimer (ISO)

sulforaphane (ISO)

tert-butyl hydroperoxide (ISO)

testosterone (EXP)

tetrachloromethane (ISO)

thapsigargin (ISO)

thiabendazole (EXP)

thioacetamide (EXP)

trichostatin A (ISO)

trovafloxacin (ISO)

urethane (ISO)

valproic acid (ISO)

vorinostat (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anatomical structure formation involved in morphogenesis (ISO)

axon extension (IEA,ISO)

axon guidance (IEA,ISO)

brain development (ISO)

cerebral cortex development (IEA,ISO)

dorsal/ventral pattern formation (IEA,ISO)

hair follicle development (IEA,ISO)

maintenance of epithelial cell apical/basal polarity (IEA,ISO)

mesoderm development (IEA,ISO)

negative regulation of gene expression, epigenetic (IEA,ISO)

negative regulation of neurogenesis (IEA,ISO)

negative regulation of transcription regulatory region DNA binding (IEA,ISO)

nervous system development (ISO)

neural tube closure (IEA,ISO)

neurogenesis (ISO)

neuron differentiation (IBA,IEP,ISO)

olfactory bulb development (IEA,ISO)

positive regulation of DNA-templated transcription (ISO,ISS)

positive regulation of neural precursor cell proliferation (IEA,ISO)

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

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

retina development in camera-type eye (IEA,ISO)

telencephalon development (ISO)

telencephalon regionalization (IEA,ISO)

Cellular Component

nucleus (IBA,IEA,ISO)

Molecular Function

chromatin binding (IEA,ISO)

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

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

metal ion binding (IEA)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA,ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IBA)

sequence-specific DNA 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.	Gene Data Set	MGD Curation, June 12, 2002
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
4.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	Lhx2, a LIM homeobox gene, is required for eye, forebrain, and definitive erythrocyte development.	Porter FD, etal., Development 1997 Aug;124(15):2935-44.
6.	GOA pipeline	RGD automated data pipeline
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
8.	Paleocortex is specified in mice in which dorsal telencephalic patterning is severely disrupted.	Vyas A, etal., J Comp Neurol 2003 Nov 24;466(4):545-53.
9.	LH-2: a LIM/homeodomain gene expressed in developing lymphocytes and neural cells.	Xu Y, etal., Proc Natl Acad Sci U S A 1993 Jan 1;90(1):227-31.

Additional References at PubMed

PMID:7513049	PMID:9697309	PMID:10431247	PMID:10482234	PMID:10593900	PMID:11165475	PMID:11719201	PMID:15173589	PMID:15295034	PMID:17005264	PMID:17493606	PMID:17991461
PMID:18076286	PMID:18184563	PMID:19146846	PMID:19820705	PMID:21857657	PMID:22457488	PMID:22734700	PMID:24012369	PMID:26371318	PMID:28053041	PMID:34581932

Genomics

Comparative Map Data

Lhx2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	22,113,619 - 22,143,909 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	22,126,007 - 22,143,908 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	25,594,877 - 25,612,777 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	3	34,179,870 - 34,197,771 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	3	31,991,800 - 32,009,717 (+)	NCBI	Rnor_WKY
Rnor_6.0	3	22,628,674 - 22,658,447 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	22,640,545 - 22,658,446 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	27,870,008 - 27,887,929 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	18,129,455 - 18,147,357 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	18,025,179 - 18,043,730 (+)	NCBI
Celera	3	20,559,471 - 20,577,366 (+)	NCBI		Celera
Cytogenetic Map	3	q12	NCBI

LHX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	124,011,768 - 124,033,301 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	9	124,001,670 - 124,033,301 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	126,774,047 - 126,795,580 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	125,813,710 - 125,835,263 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	123,853,442 - 123,874,996	NCBI
Celera	9	97,421,143 - 97,442,696 (+)	NCBI		Celera
Cytogenetic Map	9	q33.3	NCBI
HuRef	9	96,387,559 - 96,409,113 (+)	NCBI		HuRef
CHM1_1	9	126,922,665 - 126,944,218 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	9	136,209,686 - 136,231,219 (+)	NCBI		T2T-CHM13v2.0

Lhx2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	38,229,226 - 38,259,749 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	38,229,293 - 38,259,745 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	38,339,271 - 38,369,737 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	38,339,281 - 38,369,733 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	38,206,828 - 38,225,248 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	38,173,317 - 38,191,737 (+)	NCBI		MGSCv36	mm8
Celera	2	40,107,977 - 40,108,866 (+)	NCBI		Celera
Cytogenetic Map	2	B	NCBI

Lhx2
(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_004955419	3,998,242 - 4,018,875 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955419	3,999,364 - 4,019,543 (-)	NCBI	ChiLan1.0	ChiLan1.0

LHX2
(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	9	15,324,546 - 15,346,290 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	95,132,445 - 95,154,130 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	123,655,845 - 123,676,803 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	123,655,845 - 123,676,796 (+)	Ensembl	panpan1.1		panPan2

LHX2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	58,825,505 - 58,859,311 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	58,825,492 - 58,845,883 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	58,022,250 - 58,042,687 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	59,745,814 - 59,766,310 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	59,745,801 - 59,766,240 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	58,502,870 - 58,523,325 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	58,819,702 - 58,840,014 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	58,910,400 - 58,930,871 (-)	NCBI		UU_Cfam_GSD_1.0

Lhx2
(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_024404947	192,627,290 - 192,645,467 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936487	12,395,812 - 12,414,003 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936487	12,395,817 - 12,413,860 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LHX2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	264,900,591 - 264,920,890 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	264,900,931 - 264,920,888 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	298,708,264 - 298,728,222 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LHX2
(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	12	14,110,122 - 14,133,411 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	14,110,068 - 14,132,026 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666079	1,939,043 - 1,961,601 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lhx2
(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_004624760	10,951,837 - 10,982,592 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Lhx2
75 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	254
Count of miRNA genes:	133
Interacting mature miRNAs:	159
Transcripts:	ENSRNOT00000014452, ENSRNOT00000064507
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70202	Alc19	Alcohol consumption QTL 19	2.5		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	3	1	27494778	Rat
631679	Cm10	Cardiac mass QTL 10	7.34	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	1	31158234	Rat
631831	Alc8	Alcohol consumption QTL 8	2.7		consumption behavior trait (VT:0002069)	calculated ethanol drink intake rate (CMO:0001615)	3	1	33230976	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	diastolic blood pressure (CMO:0000005)	3	1	33278763	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	1	33278763	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	pulse pressure (CMO:0000292)	3	1	33278763	Rat
631545	Bp85	Blood pressure QTL 85	3.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	33278763	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	1	36847613	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	38710544	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	39874793	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	Rat
1298526	Arunc3	Aerobic running capacity QTL 3	2.2		exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	8227194	33703538	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	8227194	47233430	Rat
70203	Gcr2	Gastric cancer resistance QTL 2	2.6		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	3	8658162	27494778	Rat
1358357	Srcrtb1	Stress Responsive Cort Basal QTL 1	6.36	0.002	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	8658162	27494778	Rat
6893355	Bw101	Body weight QTL 101	0.4	0.38	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
6893363	Bw105	Body weight QTL 105	2.6	0.0036	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
1558654	Bw56	Body weight QTL 56	4.5	0.0000171	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	3	10778704	50302886	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	3	10778704	50302886	Rat
1558647	Cm46	Cardiac mass QTL 46	5.4	0.0000055	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	10778823	30356773	Rat
1558657	Cm43	Cardiac mass QTL 43	6.6	0.0000000293	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	15005422	76927699	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	16954708	61954708	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	17374703	35528639	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	17374703	35528639	Rat
2325840	Bp345	Blood pressure QTL 345		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	18311454	28441896	Rat
731172	Bp151	Blood pressure QTL 151		0.04	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	18311454	47233430	Rat
12879849	Bw180	Body weight QTL 180		0.037	body mass (VT:0001259)	body weight (CMO:0000012)	3	18311454	47233430	Rat
12879850	Cm91	Cardiac mass QTL 91		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	18311454	47233430	Rat
12879851	Cm92	Cardiac mass QTL 92		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	18311454	47233430	Rat
12879852	Cm93	Cardiac mass QTL 93		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	18311454	47233430	Rat
12879853	Am5	Aortic mass QTL 5		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	18311454	47233430	Rat
12879854	Kidm63	Kidney mass QTL 63		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	18311454	47233430	Rat
10450804	Scl70	Serum cholesterol level QTL 70	4.7	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	20714090	65714090	Rat
10450794	Scl69	Serum cholesterol level QTL 69	6.3	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	20714090	65714090	Rat

Markers in Region

D3Got17

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	22,131,405 - 22,131,609 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	22,645,944 - 22,646,147	NCBI	Rnor6.0
Rnor_5.0	3	27,875,426 - 27,875,629	UniSTS	Rnor5.0
RGSC_v3.4	3	18,134,854 - 18,135,057	RGD	RGSC3.4
RGSC_v3.4	3	18,134,854 - 18,135,057	UniSTS	RGSC3.4
RGSC_v3.1	3	18,031,226 - 18,031,429	RGD
Celera	3	20,564,870 - 20,565,073	UniSTS
RH 3.4 Map	3	224.2	RGD
RH 3.4 Map	3	224.2	UniSTS
RH 2.0 Map	3	103.6	RGD
Cytogenetic Map	3	q11	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

	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		6	6		6			68		1
Low	22	35	35	5	35	3	5	4		31		3
Below cutoff	20	9		11		5	6	2	19	5	4	5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106571	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006234072	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006234073	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008761742	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017591665	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473983	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000115	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000014452 ⟹ ENSRNOP00000014452

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	22,640,604 - 22,657,887 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000064507 ⟹ ENSRNOP00000061914

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	22,126,007 - 22,143,908 (+)	Ensembl
Rnor_6.0 Ensembl	3	22,640,545 - 22,658,446 (+)	Ensembl

RefSeq Acc Id:

NM_001106571 ⟹ NP_001100041

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	22,126,007 - 22,143,908 (+)	NCBI
Rnor_6.0	3	22,640,545 - 22,658,446 (+)	NCBI
Rnor_5.0	3	27,870,008 - 27,887,929 (+)	NCBI
RGSC_v3.4	3	18,129,455 - 18,147,357 (+)	RGD
Celera	3	20,559,471 - 20,577,366 (+)	RGD

Sequence:

show sequence

GCAGCTGAGGCGGGGGGCAAGCCCTTCCTCCGGGCAGCCGCGTCCCGGGTCCCGCCGCGATGCT
GTTCCACAGTCTGTCGGGCCCCGAGGTGCACGGGGTCATCGACGAGATGGACCGCAGGGCCAAG
AGCGAGGCTCCGGCCATCAGCTCCGCCATCGACCGCGGCGACACGGAGACGACCATGCCGTCCA
TCAGCAGTGACCGGGCAGCGTTGTGTGCGGGCTGTGGGGGCAAGATCTCTGACCGCTACTATTT
GCTGGCAGTAGACAAACAATGGCACATGCGTTGCCTCAAGTGCTGTGAATGCAAGCTCAACCTG
GAGTCGGAACTCACCTGCTTCAGCAAGGATGGCAGCATCTACTGCAAAGAAGACTACTACAGGC
GGTTCTCTGTGCAGCGCTGCGCCCGCTGCCACCTGGGCATCTCGGCCTCAGAGATGGTGATGCG
TGCTCGGGACTTGGTTTATCACCTCAACTGCTTCACATGCACCACGTGTAACAAGATGCTGACG
ACCGGCGACCACTTCGGCATGAAGGACAGCCTGGTCTATTGCCGCTTGCACTTCGAGGCACTGC
TGCAAGGCGAATACCCGGCACACTTTAACCATGCCGACGTGGCAGCGGCGGCAGCGGCAGCCGC
AGCAGCTAAGAGTGCAGGATTGGGCTCAGCTGGGGCTAACCCGCTGGGTCTTCCCTACTACAAC
GGCGTGGGCACTGTGCAGAAGGGGAGGCCGAGAAAGCGCAAAAGTCCAGGACCCGGGGCAGATC
TGGCAGCCTACAACGCCGCGCTGAGCTGTAACGAGAACGACGCGGAACACCTGGATCGCGACCA
GCCCTACCCTAGCAGCCAAAAGACAAAGCGCATGCGCACCTCCTTCAAGCACCACCAGCTTCGG
ACAATGAAGTCTTACTTTGCCATTAACCACAATCCCGATGCCAAGGACTTGAAGCAGCTCGCGC
AAAAGACCGGCCTCACCAAGAGAGTCCTCCAGGTCTGGTTTCAGAATGCCCGGGCCAAGTTCAG
GCGCAACCTTTTACGGCAGGAAAACACTGGTGTGGACAAGACTTCGGATGCCACGCTGCAGACA
GGGACACCGTCAGGGCCCGCCTCGGAGCTGTCCAACGCCTCGCTCAGCCCCTCCAGCACTCCTA
CAACCCTCACAGACTTGACTAGCCCCACCCTGCCGACTGTGACGTCAGTCTTAACTTCTGTGCC
TGGCAACCTGGAGGGCCATGAGCCCCACAGCCCTTCACAAACGACTCTTACCAACCTTTTCTAA
TGACTCGCCACCCCCTTCTCCCCTGAGCCCCCATGATTTCTTTAAAAAAGAAATTATCTTTAGT
TGAATTCCAAGTGTATTTTAAAAATAGCGGTTTGAGCAACTAACTAACCACGTTTTAGGATCTC
GCCTGGAAACAGAGGGGGAAAAAAGAATTGTGCGTCGGGCTAACGCAGCGGTGTGTGCTGAGGA
ATTACTTGGGAGATATATCTGCAACACAACATTTGTGTCCCTGTACAGTTTTGTGGACTGAGCG
AGGAAAACAACAAATAATTTAAGTTGGCTGAGAGCTTCCGTATTTTCAAAGACTGCCACGTGCC
TTAGGAATACTGTTTTATCTTCATACTTTGGATGAATTGTTCGTTTTTTTTTCTCTCCCTCTTT
TTCTCTCTGTATATTTATGACCAGAGCAAAATGTAAAAAAGGAAAAAAAAACAAAAAAACAAAA
AAAGTTTGTTACTTTGAATAGTCCTAAAGAAGAAAAAGAAAAAAAAAAAAAAACAAGGAAAAAA
ATCAAATCCCCTCCAACAGTCGCTTTCTTGTTTTAGAATTTTAAGGTGGAAGTCTGTTCGGATA
TCAGAATTTGTAAAACCTAACCAGTAATAAAATCACTTATCGAAAAG

hide sequence

RefSeq Acc Id:

XM_006234072 ⟹ XP_006234134

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	22,126,036 - 22,143,909 (+)	NCBI
Rnor_6.0	3	22,640,577 - 22,658,447 (+)	NCBI
Rnor_5.0	3	27,870,008 - 27,887,929 (+)	NCBI

Sequence:

show sequence

GGCAGCCGCGTCCCGGGTCCCGCCGCGATGCTGTTCCACAGTCTGTCGGGCCCCGAGGTGCACG
GGGTCATCGACGAGATGGACCGCAGGGCCAAGAGCGAGGCTCCGGCCATCAGCTCCGCCATCGA
CCGCGGCGACACGGAGACGACCATGCCGTCCATCAGCAGTGACCGGGCAGCGTTGTGTGCGGGC
TGTGGGGGCAAGATCTCTGACCGCTACTATTTGCTGGCAGTAGACAAACAATGGCACATGCGTT
GCCTCAAGTGCTGTGAATGCAAGCTCAACCTGGAGTCGGAACTCACCTGCTTCAGCAAGGATGG
CAGCATCTACTGCAAAGAAGACTACTACAGCCCCTCCCTCCATGGTCCCCACAGGCGGTTCTCT
GTGCAGCGCTGCGCCCGCTGCCACCTGGGCATCTCGGCCTCAGAGATGGTGATGCGTGCTCGGG
ACTTGGTTTATCACCTCAACTGCTTCACATGCACCACGTGTAACAAGATGCTGACGACCGGCGA
CCACTTCGGCATGAAGGACAGCCTGGTCTATTGCCGCTTGCACTTCGAGGCACTGCTGCAAGGC
GAATACCCGGCACACTTTAACCATGCCGACGTGGCAGCGGCGGCAGCGGCAGCCGCAGCAGCTA
AGAGTGCAGGATTGGGCTCAGCTGGGGCTAACCCGCTGGGTCTTCCCTACTACAACGGCGTGGG
CACTGTGCAGAAGGGGAGGCCGAGAAAGCGCAAAAGTCCAGGACCCGGGGCAGATCTGGCAGCC
TACAACGCCGCGCTGAGCTGTAACGAGAACGACGCGGAACACCTGGATCGCGACCAGCCCTACC
CTAGCAGCCAAAAGACAAAGCGCATGCGCACCTCCTTCAAGCACCACCAGCTTCGGACAATGAA
GTCTTACTTTGCCATTAACCACAATCCCGATGCCAAGGACTTGAAGCAGCTCGCGCAAAAGACC
GGCCTCACCAAGAGAGTCCTCCAGGTCTGGTTTCAGAATGCCCGGGCCAAGTTCAGGCGCAACC
TTTTACGGCAGGAAAACACTGGTGTGGACAAGACTTCGGATGCCACGCTGCAGACAGGGACACC
GTCAGGGCCCGCCTCGGAGCTGTCCAACGCCTCGCTCAGCCCCTCCAGCACTCCTACAACCCTC
ACAGACTTGACTAGCCCCACCCTGCCGACTGTGACGTCAGTCTTAACTTCTGTGCCTGGCAACC
TGGAGGGCCATGAGCCCCACAGCCCTTCACAAACGACTCTTACCAACCTTTTCTAATGACTCGC
CACCCCCTTCTCCCCTGAGCCCCCATGATTTCTTTAAAAAAGAAATTATCTTTAGTTGAATTCC
AAGTGTATTTTAAAAATAGCGGTTTGAGCAACTAACTAACCACGTTTTAGGATCTCGCCTGGAA
ACAGAGGGGGAAAAAAGAATTGTGCGTCGGGCTAACGCAGCGGTGTGTGCTGAGGAATTACTTG
GGAGATATATCTGCAACACAACATTTGTGTCCCTGTACAGTTTTGTGGACTGAGCGAGGAAAAC
AACAAATAATTTAAGTTGGCTGAGAGCTTCCGTATTTTCAAAGACTGCCACGTGCCTTAGGAAT
ACTGTTTTATCTTCATACTTTGGATGAATTGTTCGTTTTTTTTTCTCTCCCTCTTTTTCTCTCT
GTATATTTATGACCAGAGCAAAATGTAAAAAAGGAAAAAAAAACAAAAAAACAAAAAAAGTTTG
TTACTTTGAATAGTCCTAAAGAAGAAAAAGAAAAAAAAAAAAAAACAAGGAAAAAAATCAAATC
CCCTCCAACAGTCGCTTTCTTGTTTTAGAATTTTAAGGTGGAAGTCTGTTCGGATATCAGAATT
TGTAAAACCTAACCAGTAATAAAATCACTTATCGAAAAGA

hide sequence

RefSeq Acc Id:

XM_006234073 ⟹ XP_006234135

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	22,127,610 - 22,143,909 (+)	NCBI
Rnor_6.0	3	22,642,148 - 22,658,447 (+)	NCBI
Rnor_5.0	3	27,870,008 - 27,887,929 (+)	NCBI

Sequence:

show sequence

CCGTCCATCAGCAGTGACCGGGCAGCGTTGTGTGCGGGCTGTGGGGGCAAGATCTCTGACCGCT
ACTATTTGCTGGCAGTAGACAAACAATGGCACATGCGTTGCCTCAAGTGCTGTGAATGCAAGCT
CAACCTGGAGTCGGAACTCACCTGCTTCAGCAAGGATGGCAGCATCTACTGCAAAGAAGACTAC
TACAGCGGTGTGTAGGATTCCCAGGTGCTGGTCTGGAGGGAAGGGGCAAAGGTTGAGGAAGGGG
CGGTTCTCTGTGCAGCGCTGCGCCCGCTGCCACCTGGGCATCTCGGCCTCAGAGATGGTGATGC
GTGCTCGGGACTTGGTTTATCACCTCAACTGCTTCACATGCACCACGTGTAACAAGATGCTGAC
GACCGGCGACCACTTCGGCATGAAGGACAGCCTGGTCTATTGCCGCTTGCACTTCGAGGCACTG
CTGCAAGGCGAATACCCGGCACACTTTAACCATGCCGACGTGGCAGCGGCGGCAGCGGCAGCCG
CAGCAGCTAAGAGTGCAGGATTGGGCTCAGCTGGGGCTAACCCGCTGGGTCTTCCCTACTACAA
CGGCGTGGGCACTGTGCAGAAGGGGAGGCCGAGAAAGCGCAAAAGTCCAGGACCCGGGGCAGAT
CTGGCAGCCTACAACGCCGCGCTGAGCTGTAACGAGAACGACGCGGAACACCTGGATCGCGACC
AGCCCTACCCTAGCAGCCAAAAGACAAAGCGCATGCGCACCTCCTTCAAGCACCACCAGCTTCG
GACAATGAAGTCTTACTTTGCCATTAACCACAATCCCGATGCCAAGGACTTGAAGCAGCTCGCG
CAAAAGACCGGCCTCACCAAGAGAGTCCTCCAGGTCTGGTTTCAGAATGCCCGGGCCAAGTTCA
GGCGCAACCTTTTACGGCAGGAAAACACTGGTGTGGACAAGACTTCGGATGCCACGCTGCAGAC
AGGGACACCGTCAGGGCCCGCCTCGGAGCTGTCCAACGCCTCGCTCAGCCCCTCCAGCACTCCT
ACAACCCTCACAGACTTGACTAGCCCCACCCTGCCGACTGTGACGTCAGTCTTAACTTCTGTGC
CTGGCAACCTGGAGGGCCATGAGCCCCACAGCCCTTCACAAACGACTCTTACCAACCTTTTCTA
ATGACTCGCCACCCCCTTCTCCCCTGAGCCCCCATGATTTCTTTAAAAAAGAAATTATCTTTAG
TTGAATTCCAAGTGTATTTTAAAAATAGCGGTTTGAGCAACTAACTAACCACGTTTTAGGATCT
CGCCTGGAAACAGAGGGGGAAAAAAGAATTGTGCGTCGGGCTAACGCAGCGGTGTGTGCTGAGG
AATTACTTGGGAGATATATCTGCAACACAACATTTGTGTCCCTGTACAGTTTTGTGGACTGAGC
GAGGAAAACAACAAATAATTTAAGTTGGCTGAGAGCTTCCGTATTTTCAAAGACTGCCACGTGC
CTTAGGAATACTGTTTTATCTTCATACTTTGGATGAATTGTTCGTTTTTTTTTCTCTCCCTCTT
TTTCTCTCTGTATATTTATGACCAGAGCAAAATGTAAAAAAGGAAAAAAAAACAAAAAAACAAA
AAAAGTTTGTTACTTTGAATAGTCCTAAAGAAGAAAAAGAAAAAAAAAAAAAAACAAGGAAAAA
AATCAAATCCCCTCCAACAGTCGCTTTCTTGTTTTAGAATTTTAAGGTGGAAGTCTGTTCGGAT
ATCAGAATTTGTAAAACCTAACCAGTAATAAAATCACTTATCGAAAAGA

hide sequence

RefSeq Acc Id:

XM_008761742 ⟹ XP_008759964

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	22,126,329 - 22,143,909 (+)	NCBI
Rnor_6.0	3	22,640,763 - 22,658,447 (+)	NCBI

Sequence:

show sequence

CCTGGCGGGGCCAGCCAGCGCCTCTGTTCCCCGAACTTTAGGTAGAGTCCTCCGAGACGCACGG
GACCAAGGCTGAGGGATCCTCGGACAGGGTGCGAGGCCCCGGGCGCCAGACTCAGGGGAAACCC
GGTTGCTAGAGCGGAGGAGGGAGTCAAGGTTGAAACCCAGATCTGGACCGCGAGGGTGGAGGAG
AACGTTGTTCTAGAAGTGGAAGCGCGAGGCCACTCTCTTCTCTCTGCTCCTGGCGCTCCAGTCC
ACAGTCCTGACTCTCCACCACTACTAGGCTACCATGCCGTCCATCAGCAGTGACCGGGCAGCGT
TGTGTGCGGGCTGTGGGGGCAAGATCTCTGACCGCTACTATTTGCTGGCAGTAGACAAACAATG
GCACATGCGTTGCCTCAAGTGCTGTGAATGCAAGCTCAACCTGGAGTCGGAACTCACCTGCTTC
AGCAAGGATGGCAGCATCTACTGCAAAGAAGACTACTACAGCCCCTCCCTCCATGGTCCCCACA
GGCGGTTCTCTGTGCAGCGCTGCGCCCGCTGCCACCTGGGCATCTCGGCCTCAGAGATGGTGAT
GCGTGCTCGGGACTTGGTTTATCACCTCAACTGCTTCACATGCACCACGTGTAACAAGATGCTG
ACGACCGGCGACCACTTCGGCATGAAGGACAGCCTGGTCTATTGCCGCTTGCACTTCGAGGCAC
TGCTGCAAGGCGAATACCCGGCACACTTTAACCATGCCGACGTGGCAGCGGCGGCAGCGGCAGC
CGCAGCAGCTAAGAGTGCAGGATTGGGCTCAGCTGGGGCTAACCCGCTGGGTCTTCCCTACTAC
AACGGCGTGGGCACTGTGCAGAAGGGGAGGCCGAGAAAGCGCAAAAGTCCAGGACCCGGGGCAG
ATCTGGCAGCCTACAACGCCGCGCTGAGCTGTAACGAGAACGACGCGGAACACCTGGATCGCGA
CCAGCCCTACCCTAGCAGCCAAAAGACAAAGCGCATGCGCACCTCCTTCAAGCACCACCAGCTT
CGGACAATGAAGTCTTACTTTGCCATTAACCACAATCCCGATGCCAAGGACTTGAAGCAGCTCG
CGCAAAAGACCGGCCTCACCAAGAGAGTCCTCCAGGTCTGGTTTCAGAATGCCCGGGCCAAGTT
CAGGCGCAACCTTTTACGGCAGGAAAACACTGGTGTGGACAAGACTTCGGATGCCACGCTGCAG
ACAGGGACACCGTCAGGGCCCGCCTCGGAGCTGTCCAACGCCTCGCTCAGCCCCTCCAGCACTC
CTACAACCCTCACAGACTTGACTAGCCCCACCCTGCCGACTGTGACGTCAGTCTTAACTTCTGT
GCCTGGCAACCTGGAGGGCCATGAGCCCCACAGCCCTTCACAAACGACTCTTACCAACCTTTTC
TAATGACTCGCCACCCCCTTCTCCCCTGAGCCCCCATGATTTCTTTAAAAAAGAAATTATCTTT
AGTTGAATTCCAAGTGTATTTTAAAAATAGCGGTTTGAGCAACTAACTAACCACGTTTTAGGAT
CTCGCCTGGAAACAGAGGGGGAAAAAAGAATTGTGCGTCGGGCTAACGCAGCGGTGTGTGCTGA
GGAATTACTTGGGAGATATATCTGCAACACAACATTTGTGTCCCTGTACAGTTTTGTGGACTGA
GCGAGGAAAACAACAAATAATTTAAGTTGGCTGAGAGCTTCCGTATTTTCAAAGACTGCCACGT
GCCTTAGGAATACTGTTTTATCTTCATACTTTGGATGAATTGTTCGTTTTTTTTTCTCTCCCTC
TTTTTCTCTCTGTATATTTATGACCAGAGCAAAATGTAAAAAAGGAAAAAAAAACAAAAAAACA
AAAAAAGTTTGTTACTTTGAATAGTCCTAAAGAAGAAAAAGAAAAAAAAAAAAAAACAAGGAAA
AAAATCAAATCCCCTCCAACAGTCGCTTTCTTGTTTTAGAATTTTAAGGTGGAAGTCTGTTCGG
ATATCAGAATTTGTAAAACCTAACCAGTAATAAAATCACTTATCGAAAAGA

hide sequence

RefSeq Acc Id:

XM_017591665 ⟹ XP_017447154

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	22,113,619 - 22,143,909 (+)	NCBI
Rnor_6.0	3	22,628,674 - 22,658,447 (+)	NCBI

Sequence:

show sequence

GCTGCACGAGGGGCTCACCAAGACCATGCCGTCCATCAGCAGTGACCGGGCAGCGTTGTGTGCG
GGCTGTGGGGGCAAGATCTCTGACCGCTACTATTTGCTGGCAGTAGACAAACAATGGCACATGC
GTTGCCTCAAGTGCTGTGAATGCAAGCTCAACCTGGAGTCGGAACTCACCTGCTTCAGCAAGGA
TGGCAGCATCTACTGCAAAGAAGACTACTACAGCCCCTCCCTCCATGGTCCCCACAGGCGGTTC
TCTGTGCAGCGCTGCGCCCGCTGCCACCTGGGCATCTCGGCCTCAGAGATGGTGATGCGTGCTC
GGGACTTGGTTTATCACCTCAACTGCTTCACATGCACCACGTGTAACAAGATGCTGACGACCGG
CGACCACTTCGGCATGAAGGACAGCCTGGTCTATTGCCGCTTGCACTTCGAGGCACTGCTGCAA
GGCGAATACCCGGCACACTTTAACCATGCCGACGTGGCAGCGGCGGCAGCGGCAGCCGCAGCAG
CTAAGAGTGCAGGATTGGGCTCAGCTGGGGCTAACCCGCTGGGTCTTCCCTACTACAACGGCGT
GGGCACTGTGCAGAAGGGGAGGCCGAGAAAGCGCAAAAGTCCAGGACCCGGGGCAGATCTGGCA
GCCTACAACGCCGCGCTGAGCTGTAACGAGAACGACGCGGAACACCTGGATCGCGACCAGCCCT
ACCCTAGCAGCCAAAAGACAAAGCGCATGCGCACCTCCTTCAAGCACCACCAGCTTCGGACAAT
GAAGTCTTACTTTGCCATTAACCACAATCCCGATGCCAAGGACTTGAAGCAGCTCGCGCAAAAG
ACCGGCCTCACCAAGAGAGTCCTCCAGGTCTGGTTTCAGAATGCCCGGGCCAAGTTCAGGCGCA
ACCTTTTACGGCAGGAAAACACTGGTGTGGACAAGACTTCGGATGCCACGCTGCAGACAGGGAC
ACCGTCAGGGCCCGCCTCGGAGCTGTCCAACGCCTCGCTCAGCCCCTCCAGCACTCCTACAACC
CTCACAGACTTGACTAGCCCCACCCTGCCGACTGTGACGTCAGTCTTAACTTCTGTGCCTGGCA
ACCTGGAGGGCCATGAGCCCCACAGCCCTTCACAAACGACTCTTACCAACCTTTTCTAATGACT
CGCCACCCCCTTCTCCCCTGAGCCCCCATGATTTCTTTAAAAAAGAAATTATCTTTAGTTGAAT
TCCAAGTGTATTTTAAAAATAGCGGTTTGAGCAACTAACTAACCACGTTTTAGGATCTCGCCTG
GAAACAGAGGGGGAAAAAAGAATTGTGCGTCGGGCTAACGCAGCGGTGTGTGCTGAGGAATTAC
TTGGGAGATATATCTGCAACACAACATTTGTGTCCCTGTACAGTTTTGTGGACTGAGCGAGGAA
AACAACAAATAATTTAAGTTGGCTGAGAGCTTCCGTATTTTCAAAGACTGCCACGTGCCTTAGG
AATACTGTTTTATCTTCATACTTTGGATGAATTGTTCGTTTTTTTTTCTCTCCCTCTTTTTCTC
TCTGTATATTTATGACCAGAGCAAAATGTAAAAAAGGAAAAAAAAACAAAAAAACAAAAAAAGT
TTGTTACTTTGAATAGTCCTAAAGAAGAAAAAGAAAAAAAAAAAAAAACAAGGAAAAAAATCAA
ATCCCCTCCAACAGTCGCTTTCTTGTTTTAGAATTTTAAGGTGGAAGTCTGTTCGGATATCAGA
ATTTGTAAAACCTAACCAGTAATAAAATCACTTATCGAAAAGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001100041	(Get FASTA)	NCBI Sequence Viewer
	XP_006234134	(Get FASTA)	NCBI Sequence Viewer
	XP_006234135	(Get FASTA)	NCBI Sequence Viewer
	XP_008759964	(Get FASTA)	NCBI Sequence Viewer
	XP_017447154	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM00518	(Get FASTA)	NCBI Sequence Viewer
	P36198	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001100041 ⟸ NM_001106571

- UniProtKB:

D4A380 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLFHSLSGPEVHGVIDEMDRRAKSEAPAISSAIDRGDTETTMPSISSDRAALCAGCGGKISDRY
YLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDYYRRFSVQRCARCHLGISASEMV
MRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDSLVYCRLHFEALLQGEYPAHFNHADVAAAAAA
AAAAKSAGLGSAGANPLGLPYYNGVGTVQKGRPRKRKSPGPGADLAAYNAALSCNENDAEHLDR
DQPYPSSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK
FRRNLLRQENTGVDKTSDATLQTGTPSGPASELSNASLSPSSTPTTLTDLTSPTLPTVTSVLTS
VPGNLEGHEPHSPSQTTLTNLF

hide sequence

RefSeq Acc Id:	XP_006234134 ⟸ XM_006234072
- Peptide Label:	isoform X1
- UniProtKB:	D4A380 (UniProtKB/TrEMBL)
- Sequence:	show sequence MLFHSLSGPEVHGVIDEMDRRAKSEAPAISSAIDRGDTETTMPSISSDRAALCAGCGGKISDRY YLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDYYSPSLHGPHRRFSVQRCARCHL GISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDSLVYCRLHFEALLQGEYPAHFNHA DVAAAAAAAAAAKSAGLGSAGANPLGLPYYNGVGTVQKGRPRKRKSPGPGADLAAYNAALSCNE NDAEHLDRDQPYPSSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQV WFQNARAKFRRNLLRQENTGVDKTSDATLQTGTPSGPASELSNASLSPSSTPTTLTDLTSPTLP TVTSVLTSVPGNLEGHEPHSPSQTTLTNLF hide sequence

RefSeq Acc Id:

XP_006234135 ⟸ XM_006234073

- Peptide Label:

isoform X3

- Sequence:

show sequence

MAASTAKKTTTAVCRIPRCWSGGKGQRLRKGRFSVQRCARCHLGISASEMVMRARDLVYHLNCF
TCTTCNKMLTTGDHFGMKDSLVYCRLHFEALLQGEYPAHFNHADVAAAAAAAAAAKSAGLGSAG
ANPLGLPYYNGVGTVQKGRPRKRKSPGPGADLAAYNAALSCNENDAEHLDRDQPYPSSQKTKRM
RTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENTGV
DKTSDATLQTGTPSGPASELSNASLSPSSTPTTLTDLTSPTLPTVTSVLTSVPGNLEGHEPHSP
SQTTLTNLF

hide sequence

RefSeq Acc Id:

XP_008759964 ⟸ XM_008761742

- Peptide Label:

isoform X2

- Sequence:

show sequence

MPSISSDRAALCAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKED
YYSPSLHGPHRRFSVQRCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDS
LVYCRLHFEALLQGEYPAHFNHADVAAAAAAAAAAKSAGLGSAGANPLGLPYYNGVGTVQKGRP
RKRKSPGPGADLAAYNAALSCNENDAEHLDRDQPYPSSQKTKRMRTSFKHHQLRTMKSYFAINH
NPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENTGVDKTSDATLQTGTPSGPASEL
SNASLSPSSTPTTLTDLTSPTLPTVTSVLTSVPGNLEGHEPHSPSQTTLTNLF

hide sequence

RefSeq Acc Id:

XP_017447154 ⟸ XM_017591665

- Peptide Label:

isoform X2

- Sequence:

show sequence

MPSISSDRAALCAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKED
YYSPSLHGPHRRFSVQRCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDS
LVYCRLHFEALLQGEYPAHFNHADVAAAAAAAAAAKSAGLGSAGANPLGLPYYNGVGTVQKGRP
RKRKSPGPGADLAAYNAALSCNENDAEHLDRDQPYPSSQKTKRMRTSFKHHQLRTMKSYFAINH
NPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENTGVDKTSDATLQTGTPSGPASEL
SNASLSPSSTPTTLTDLTSPTLPTVTSVLTSVPGNLEGHEPHSPSQTTLTNLF

hide sequence

RefSeq Acc Id:

ENSRNOP00000014452 ⟸ ENSRNOT00000014452

RefSeq Acc Id:

ENSRNOP00000061914 ⟸ ENSRNOT00000064507

Protein Domains

Homeobox LIM zinc-binding

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P36198-F1-model_v2	AlphaFold	P36198	1-426	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:71076	AgrOrtholog
BioCyc Gene	G2FUF-49914	BioCyc
Ensembl Genes	ENSRNOG00000010551	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000061914	ENTREZGENE
	ENSRNOP00000061914.2	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000064507	ENTREZGENE
	ENSRNOT00000064507.4	UniProtKB/TrEMBL
Gene3D-CATH	Cysteine Rich Protein	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_LIM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:296706	UniProtKB/TrEMBL
NCBI Gene	296706	ENTREZGENE
PANTHER	LIM/HOMEOBOX PROTEIN LHX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LIM/HOMEOBOX PROTEIN LHX2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LIM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Lhx2	PhenoGen
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LIM_DOMAIN_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LIM_DOMAIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	HOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LIM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	Glucocorticoid receptor-like (DNA-binding domain)	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF46689	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	D4A380	ENTREZGENE, UniProtKB/TrEMBL
	LHX2_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-26	Lhx2	LIM homeobox 2	Lhx2	LIM homeobox protein 2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-06-09	Lhx2	LIM homeobox protein 2	Lhx2_predicted	LIM homeobox protein 2 (predicted)	Data Merged	737654	APPROVED
2005-01-12	Lhx2_predicted	LIM homeobox protein 2 (predicted)			Symbol and Name status set to approved	70820	APPROVED
2002-07-09	Lhx2	LIM homeobox protein 2			Symbol and Name updated to reflect Human and Mouse nomenclature	70877	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains a homeodomain and two repeats of a LIM domain	70777
gene_protein	426 amino acids	70777

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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