Lmx1b (LIM homeobox transcription factor 1 beta)

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Gene: Lmx1b (LIM homeobox transcription factor 1 beta) Rattus norvegicus

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Symbol:

Lmx1b

Name:

LIM homeobox transcription factor 1 beta

RGD ID:

620843

Description:

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including memory; olfactory behavior; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including collagen fibril organization; nervous system development; and trabecular meshwork development. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in nail-patella syndrome. Orthologous to human LMX1B (LIM homeobox transcription factor 1 beta); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LIM homeobox transcription factor 1-beta

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):	LMX1B (LIM homeobox transcription factor 1 beta)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Lmx1b (LIM homeobox transcription factor 1 beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lmx1b (LIM homeobox transcription factor 1 beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LMX1B (LIM homeobox transcription factor 1 beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LMX1B (LIM homeobox transcription factor 1 beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lmx1b (LIM homeobox transcription factor 1 beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LMX1B (LIM homeobox transcription factor 1 beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LMX1B (LIM homeobox transcription factor 1 beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lmx1b (LIM homeobox transcription factor 1 beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	LMX1B (LIM homeobox transcription factor 1 beta)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Lmx1b (LIM homeobox transcription factor 1 beta)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	lmx1bb (LIM homeobox transcription factor 1, beta b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	lim-6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG4328	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Lmx1a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	lmx1b.1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|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
GRCr8	3	37,257,025 - 37,338,675 (-)	NCBI		GRCr8
mRatBN7.2	3	16,862,195 - 16,940,899 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	16,862,195 - 16,940,899 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	19,930,667 - 20,009,835 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	28,515,689 - 28,594,855 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	26,766,677 - 26,845,838 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	12,608,748 - 12,686,937 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	12,609,574 - 12,686,869 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	17,938,969 - 18,018,269 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	12,571,947 - 12,651,590 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	12,470,843 - 12,473,304 (-)	NCBI
Celera	3	11,596,841 - 11,674,265 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

clubfoot (ISO)

developmental and epileptic encephalopathy (ISO)

developmental and epileptic encephalopathy 31A (ISO)

disease of mental health (ISO)

early infantile epileptic encephalopathy (ISO)

familial hyperlipidemia (ISO)

focal segmental glomerulosclerosis (ISO)

genetic disease (ISO)

Hematuria (ISO)

kidney disease (ISO)

lipoid nephrosis (ISO)

nail-patella syndrome (ISO,ISS)

nephrotic syndrome (ISO)

Neurodevelopmental Disorders (ISO)

Osteoarthritis, Hip (ISO)

proteinuria (ISO)

Salcedo Syndrome (ISO)

Sleep Initiation and Maintenance Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dimethylhydrazine (ISO)

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

3,3',5,5'-tetrabromobisphenol A (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

aflatoxin M1 (ISO)

all-trans-retinoic acid (ISO)

alpha-Zearalanol (EXP)

ammonium chloride (EXP)

atrazine (EXP)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (ISO)

calcitriol (ISO)

carmustine (ISO)

chlorpyrifos (ISO)

dieldrin (ISO)

ethylparaben (ISO)

folic acid (ISO)

lead(0) (ISO)

lipopolysaccharide (ISO)

methapyrilene (ISO)

mono(2-ethylhexyl) phthalate (ISO)

morphine (ISO)

nickel sulfate (ISO)

paracetamol (EXP,ISO)

perfluorohexanesulfonic acid (ISO)

perfluorooctanoic acid (EXP)

resveratrol (ISO)

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

simazine (ISO)

tetrachloromethane (EXP)

titanium dioxide (ISO)

trichloroethene (EXP)

triptonide (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

camera-type eye development (ISO)

cell population proliferation (ISO)

central nervous system neuron development (ISO)

cerebellum morphogenesis (ISO)

collagen fibril organization (ISO)

dopaminergic neuron differentiation (ISO)

dorsal/ventral pattern formation (ISO)

limb morphogenesis (ISO)

locomotory behavior (ISO)

memory (ISO)

midbrain development (ISO)

neuron differentiation (IBA,ISO)

neuron migration (ISO)

olfactory behavior (ISO)

organ growth (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of autophagy (ISO)

regulation of DNA-templated transcription (ISO)

regulation of gene expression (ISO)

regulation of intracellular transport (ISO)

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

synapse organization (ISO)

trabecular meshwork development (ISO)

Cellular Component

nucleus (IBA,ISO)

Molecular Function

DNA-binding transcription factor activity (ISO)

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

metal ion binding (IEA)

protein binding (ISO)

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

sequence-specific double-stranded DNA binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome.	Dreyer SD, etal., Nat Genet. 1998 May;19(1):47-50.
2.	The human LMX1B gene: transcription unit, promoter, and pathogenic mutations.	Dunston JA, etal., Genomics. 2004 Sep;84(3):565-76.
3.	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.
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
7.	GOA pipeline	RGD automated data pipeline
8.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
10.	Comprehensive gene review and curation	RGD comprehensive gene curation
11.	A second independent pathway for development of mesencephalic dopaminergic neurons requires Lmx1b.	Smidt MP, etal., Nat Neurosci 2000 Apr;3(4):337-41.

Additional References at PubMed

PMID:10660670	PMID:10767331	PMID:12897786	PMID:15229182	PMID:17151281	PMID:17166916	PMID:18076286	PMID:19951692	PMID:20568247	PMID:20589901	PMID:21752929	PMID:24399192
PMID:24785190	PMID:25915474

Genomics

Comparative Map Data

Lmx1b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	37,257,025 - 37,338,675 (-)	NCBI		GRCr8
mRatBN7.2	3	16,862,195 - 16,940,899 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	16,862,195 - 16,940,899 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	19,930,667 - 20,009,835 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	28,515,689 - 28,594,855 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	26,766,677 - 26,845,838 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	12,608,748 - 12,686,937 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	12,609,574 - 12,686,869 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	17,938,969 - 18,018,269 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	12,571,947 - 12,651,590 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	12,470,843 - 12,473,304 (-)	NCBI
Celera	3	11,596,841 - 11,674,265 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

LMX1B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	126,613,928 - 126,701,032 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	126,613,928 - 126,701,032 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	129,376,207 - 129,463,311 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	128,416,619 - 128,498,551 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	126,456,351 - 126,538,284	NCBI
Celera	9	100,030,360 - 100,115,686 (+)	NCBI		Celera
Cytogenetic Map	9	q33.3	NCBI
HuRef	9	98,989,870 - 99,079,726 (+)	NCBI		HuRef
CHM1_1	9	129,527,362 - 129,614,009 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	9	138,819,355 - 138,906,454 (+)	NCBI		T2T-CHM13v2.0

Lmx1b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	33,450,977 - 33,531,219 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	33,450,977 - 33,530,620 (-)	Ensembl		GRCm39 Ensembl
GRCm38	2	33,560,965 - 33,641,208 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	33,560,965 - 33,640,608 (-)	Ensembl	GRCm38		mm10	GRCm38
GRCm38.p6 Ensembl	2	33,560,965 - 33,640,511 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	33,420,056 - 33,496,031 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	33,386,645 - 33,462,520 (-)	NCBI		MGSCv36	mm8
Celera	2	33,269,132 - 33,345,093 (-)	NCBI		Celera
Cytogenetic Map	2	B	NCBI
cM Map	2	22.48	NCBI

Lmx1b
(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	1,782,566 - 1,857,375 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955419	1,782,566 - 1,857,375 (-)	NCBI	ChiLan1.0	ChiLan1.0

LMX1B
(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	11	12,654,414 - 12,744,054 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	12,656,759 - 12,746,399 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	97,730,850 - 97,820,554 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	126,240,722 - 126,322,716 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	126,240,722 - 126,322,420 (+)	Ensembl	panpan1.1		panPan2

LMX1B
(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	56,542,844 - 56,625,609 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	56,542,826 - 56,625,530 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	55,744,662 - 55,827,799 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	57,463,555 - 57,546,781 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	57,467,707 - 57,547,344 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	56,222,283 - 56,305,769 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	56,538,211 - 56,621,349 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	56,629,212 - 56,712,418 (-)	NCBI		UU_Cfam_GSD_1.0

Lmx1b
(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	194,744,769 - 194,819,262 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936487	14,513,290 - 14,587,902 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936487	14,513,303 - 14,587,771 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LMX1B
(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	267,207,419 - 267,287,729 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	267,207,273 - 267,290,862 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	301,155,404 - 301,230,939 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LMX1B
(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	11,443,253 - 11,526,789 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	11,444,324 - 11,526,552 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666079	4,658,674 - 4,746,282 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lmx1b
(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_004624760	8,698,139 - 8,772,147 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624760	8,701,204 - 8,772,147 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Lmx1b
542 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	75
Count of miRNA genes:	67
Interacting mature miRNAs:	75
Transcripts:	ENSRNOT00000022953
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
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
11528620	Bss113	Bone structure and strength QTL 113	9.75	2e-10	femur morphology trait (VT:0000559)	femoral neck width (CMO:0001695)	3	16490648	19241681	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
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
8693641	Alc30	Alcohol consumption QTL 30	2	0.739	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	3	10434306	24512004	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
1558657	Cm43	Cardiac mass QTL 43	6.6	3e-08	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	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
6893363	Bw105	Body weight QTL 105	2.6	0.0036	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	pulse pressure (CMO:0000292)	3	1	33278763	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
1558647	Cm46	Cardiac mass QTL 46	5.4	0.0000055	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	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
1558654	Bw56	Body weight QTL 56	4.5	0.0000171	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	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
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	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
631545	Bp85	Blood pressure QTL 85	3.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	33278763	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
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
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	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
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
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	38710544	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

Markers in Region

D3Got11

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	16,875,647 - 16,875,862 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	12,622,203 - 12,622,417	NCBI	Rnor6.0
Rnor_5.0	3	17,953,540 - 17,953,754	UniSTS	Rnor5.0
RGSC_v3.4	3	12,584,673 - 12,584,888	RGD	RGSC3.4
RGSC_v3.4	3	12,584,674 - 12,584,888	UniSTS	RGSC3.4
RGSC_v3.1	3	12,481,046 - 12,481,260	RGD
Celera	3	11,610,296 - 11,610,510	UniSTS
RH 3.4 Map	3	122.6	UniSTS
RH 3.4 Map	3	122.6	RGD
RH 2.0 Map	3	0.0	RGD
Cytogenetic Map	3	p11	UniSTS

AU049321

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	16,877,744 - 16,877,891 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	12,624,300 - 12,624,446	NCBI	Rnor6.0
Rnor_5.0	3	17,955,637 - 17,955,783	UniSTS	Rnor5.0
RGSC_v3.4	3	12,586,771 - 12,586,917	UniSTS	RGSC3.4
Celera	3	11,612,393 - 11,612,539	UniSTS
Cytogenetic Map	3	p11	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
5	6	22	83	56	57	43	4	43	6	132	35	75	45	47	14

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053709	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017591431	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063282994	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF390073	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY169317	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000022953 ⟹ ENSRNOP00000022953

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	16,862,195 - 16,940,899 (-)	Ensembl
Rnor_6.0 Ensembl	3	12,609,574 - 12,686,869 (-)	Ensembl

RefSeq Acc Id:

NM_053709 ⟹ NP_446161

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	37,259,855 - 37,338,557 (-)	NCBI
mRatBN7.2	3	16,862,195 - 16,940,899 (-)	NCBI
Rnor_6.0	3	12,608,748 - 12,686,937 (-)	NCBI
Celera	3	11,596,841 - 11,674,265 (-)	NCBI

Sequence:

show sequence

CGGAGCGGGCGGACGGACCGGAGGGCGAGCGGCCCAGCCGGCGGGGTCCGCAGCGCGCCCGGCG
TCCCATGGATATAGCAACAGGTCCCGAGTCGCTGGAGAGGTGCTTCCCTCGCGGGCAGACGGAC
TGCGCCAAGATGTTGGACGGCATCAAGATGGAGGAGCACGCCCTACGCCCCGGGCCCGCCACCC
TGGGTGTGCTGCTGGGCTCCGACTGCCCGCATCCCGCCGTCTGCGAGGGCTGCCAGCGGCCCAT
CTCCGACCGCTTCCTGATGCGAGTCAACGAGTCGTCCTGGCACGAGGAGTGTTTGCAGTGCGCG
GCATGTCAGCAAGCCCTCACCACCAGCTGCTACTTCCGGGATCGGAAACTGTACTGCAAACAAG
ACTACCAACAGCTCTTCGCGGCAAAGTGCAGCGGCTGCATGGAGAAGATCGCACCCACTGAGTT
CGTCATGCGGGCGCTCGAGTGTGTGTACCACCTGGGCTGTTTCTGCTGCTGTGTGTGCGAGAGG
CAGCTGCGGAAGGGTGATGAGTTCGTGCTCAAGGAGGGCCAGCTGCTGTGCAAGGGTGACTACG
AGAAGGAGAAAGACCTCCTCAGCTCCGTGAGCCCGGATGAGTCTGACTCTGTGAAGAGTGAGGA
TGAAGATGGAGACATGAAGCCAGCCAAGGGGCAGGGCAGCCAGAATAAGGGCAGTGGGGATGAC
GGGAAGGACCCGAGAAGGCCCAAACGGCCCCGGACCATCCTCACCACACAGCAGCGAAGAGCTT
TCAAGGCTTCGTTTGAGGTCTCCTCCAAGCCCTGTCGGAAGGTCCGAGAGACACTAGCCGCAGA
GACAGGCCTCAGTGTGCGTGTGGTCCAGGTCTGGTTTCAGAACCAAAGAGCAAAGATGAAGAAG
CTGGCCCGGAGGCACCAGCAACAGCAAGAGCAGCAGAACTCCCAGCGGCTGGGCCAAGAGGTTC
TGTCAAGCCGCATGGAGGGCATGATGGCCTCCTACACGCCGCTGGCCCCTCCGCAGCAGCAGAT
CGTGGCCATGGAGCAGAGCCCCTACGGAAGCAGCGACCCCTTCCAGCAGGGCCTCACGCCGCCC
CAAATGCCAGGTGACCACATGAACCCCTATGGAAATGACTCCATTTTCCACGATATCGATAGTG
ATACCTCCCTCACCAGCCTCAGCGACTGCTTCCTCGGCTCTTCCGACGTGGGCTCCCTGCAGGC
CCGTGTGGGGAACCCCATCGACCGGCTCTACTCCATGCAGAGCTCCTACTTTGCCTCCTGAGAG
CCGGCTGGGCCGCATGGACGCTTGGGCCTGGGCCTAGGGTGGGACCACAGGCCTCTGCAGCCAG
CCGGCCCCCCAGCCCGCCACCCGCTCAGACTCTACAGACAGCCATACGGTGCCCTCCCCTCGGC
CAGCCAGACCTGGCTCAAGTGCCCGCCGGGCACAGCCAGACAAGGCAGATGGGTGCAGCCTGGG
CAGGGACTGTGTCCTGCCCACAGAGACCTTGTGACCCCTGGGGACCCAGAGCTCTTGGACAGCC
ACTCGCCTCCCAGCCCTGTGACTTCGTCACTACCTTCCCCGTCCCCAACTCTTTTTTGGGGAAG
CTTAAATTTGTTCTTCTTTCGTTGTTTTTTTAAACATTCTGTTTTCAGCCAACCTCCATTGTCC
CTGCAAGGCCAGCCCTGGGACAGTGCCTGGTACCTGAGAAACAGTTATACGGGTGTCCTGCGCT
GGAGACCACTTCCCCTTCTGGTCAGCGCAGGGGATGGTTTCTGGGTCCTAGGAGGCCCAGGGTC
ACTGTTTCCAGCTCTAAGCTGGAGCACAGGAGAGGAGGGCCCATGCAGGTGTGGCAGGCTCTTT
GGCCCTGCCTGAACCCTAGTCTCCACAAGAGGAGGGATGTGGACAGAGCCCAGAGAGACCCAGA
GGGACAGAGATGCACACATAAAGCCACACACACCTGAAGGCACACCTGTGCAAGCATGCATGTG
CACCTGGGTGCACAGGCACACGCAGTGGAAGAGGTTGCCATTCCTTCCAGGAAGCAGAGCGAGA
TCAGTGGGTAGGGCCTACCTCTGAGAGCAATTGGAGAGGGAGGGGGGGAGGCCTG

hide sequence

RefSeq Acc Id:

XM_063282994 ⟹ XP_063139064

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	37,257,025 - 37,338,675 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_446161	(Get FASTA)	NCBI Sequence Viewer
	XP_063139064	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAK70500	(Get FASTA)	NCBI Sequence Viewer
	AAO17712	(Get FASTA)	NCBI Sequence Viewer
	EDL93185	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000022953.6

RefSeq Acc Id:

NP_446161 ⟸ NM_053709

- UniProtKB:

G3V877 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MDIATGPESLERCFPRGQTDCAKMLDGIKMEEHALRPGPATLGVLLGSDCPHPAVCEGCQRPIS
DRFLMRVNESSWHEECLQCAACQQALTTSCYFRDRKLYCKQDYQQLFAAKCSGCMEKIAPTEFV
MRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDE
DGDMKPAKGQGSQNKGSGDDGKDPRRPKRPRTILTTQQRRAFKASFEVSSKPCRKVRETLAAET
GLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQEVLSSRMEGMMASYTPLAPPQQQIV
AMEQSPYGSSDPFQQGLTPPQMPGDHMNPYGNDSIFHDIDSDTSLTSLSDCFLGSSDVGSLQAR
VGNPIDRLYSMQSSYFAS

hide sequence

Ensembl Acc Id:

ENSRNOP00000022953 ⟸ ENSRNOT00000022953

RefSeq Acc Id:	XP_063139064 ⟸ XM_063282994
- Peptide Label:	isoform X1

Protein Domains

Homeobox LIM zinc-binding

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-G3V877-F1-model_v2	AlphaFold	G3V877	1-395	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:620843	AgrOrtholog
BioCyc Gene	G2FUF-50098	BioCyc
Ensembl Genes	ENSRNOG00000017019	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000022953.7	UniProtKB/TrEMBL
Gene3D-CATH	Cysteine Rich Protein	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox_CS	UniProtKB/TrEMBL
	Homeodomain	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	LIM_Homeobox_TF	UniProtKB/TrEMBL
	Znf_LIM	UniProtKB/TrEMBL
KEGG Report	rno:114501	UniProtKB/TrEMBL
NCBI Gene	114501	ENTREZGENE
PANTHER	LIM HOMEOBOX TRANSCRIPTION FACTOR 1 ALPHA, ISOFORM B	UniProtKB/TrEMBL
	LIM HOMEOBOX TRANSCRIPTION FACTOR 1-BETA	UniProtKB/TrEMBL
	LIM/HOMEOBOX PROTEIN LHX	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
	LIM	UniProtKB/TrEMBL
PhenoGen	Lmx1b	PhenoGen
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
	LIM_DOMAIN_1	UniProtKB/TrEMBL
	LIM_DOMAIN_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000017019	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
	LIM	UniProtKB/TrEMBL
Superfamily-SCOP	Glucocorticoid receptor-like (DNA-binding domain)	UniProtKB/TrEMBL
	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A6JUB2_RAT	UniProtKB/TrEMBL
	G3V877	ENTREZGENE, UniProtKB/TrEMBL
	Q91XM6_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Lmx1b	LIM homeobox transcription factor 1 beta			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Lmx1b	LIM homeobox transcription factor 1 beta			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	enriched in mesencephalic dopamine (mesDA) systems in the substantia nigra pars compacta (SNc) and ventral tegmental area of embryos and adults	724433

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 - MGI

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