Lhx1 (LIM homeobox 1) - Rat Genome Database

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Gene: Lhx1 (LIM homeobox 1) Rattus norvegicus
Analyze
Symbol: Lhx1
Name: LIM homeobox 1
RGD ID: 71074
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and cis-regulatory region sequence-specific DNA binding activity. Involved in cellular response to fibroblast growth factor stimulus and kidney development. Located in nucleus. Orthologous to human LHX1 (LIM homeobox 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeobox protein Lim-1; LIM homeobox protein 1; LIM/homeobox protein Lhx1; rlim
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21069,396,829 - 69,403,617 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1069,396,829 - 69,403,617 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1074,016,816 - 74,023,604 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01073,521,849 - 73,528,637 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01068,986,264 - 68,993,052 (-)NCBIRnor_WKY
Rnor_6.01071,843,991 - 71,849,293 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1071,843,991 - 71,849,293 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01071,752,917 - 71,758,219 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41072,800,497 - 72,805,799 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11072,814,866 - 72,820,169 (-)NCBI
Celera1068,324,814 - 68,330,116 (-)NCBICelera
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure formation involved in morphogenesis  (ISO,ISS)
anatomical structure morphogenesis  (ISO,ISS)
anterior/posterior axis specification  (ISO,ISS)
anterior/posterior pattern specification  (ISO,ISS)
branching involved in ureteric bud morphogenesis  (ISO)
cell differentiation  (ISO)
cell-cell signaling  (ISO,ISS)
cellular response to fibroblast growth factor stimulus  (IEP)
cerebellar Purkinje cell differentiation  (ISO,ISS)
cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation  (ISO,ISS)
cerebellum development  (ISO,ISS)
cervix development  (ISO,ISS)
comma-shaped body morphogenesis  (ISO,ISS)
dorsal/ventral pattern formation  (ISO,ISS)
ectoderm formation  (ISO,ISS)
embryonic pattern specification  (ISO,ISS)
embryonic retina morphogenesis in camera-type eye  (ISO,ISS)
embryonic viscerocranium morphogenesis  (ISO,ISS)
endoderm development  (ISO)
endoderm formation  (ISO,ISS)
epithelium development  (ISO,ISS)
forebrain regionalization  (ISO,ISS)
gastrulation with mouth forming second  (ISO,ISS)
head development  (ISO,ISS)
horizontal cell localization  (ISO)
kidney development  (ISO,ISS)
lateral motor column neuron migration  (ISO,ISS)
mesendoderm development  (ISO)
mesonephric duct development  (IEP)
mesonephric tubule development  (IEP)
mesonephros development  (ISO)
metanephric comma-shaped body morphogenesis  (IEP)
metanephric glomerulus development  (IEP)
metanephric part of ureteric bud development  (IEP)
metanephric renal vesicle morphogenesis  (ISO)
metanephric S-shaped body morphogenesis  (IEP,ISO)
metanephros development  (ISO)
motor neuron axon guidance  (ISO,ISS)
negative regulation of DNA-templated transcription  (ISO,ISS)
nephric duct elongation  (ISO)
nephric duct morphogenesis  (ISO,ISS)
neuron differentiation  (IBA)
oviduct development  (ISO,ISS)
oviduct epithelium development  (ISO,ISS)
paramesonephric duct development  (ISO,ISS)
pattern specification process  (ISO,ISS)
positive regulation of anterior head development  (ISO,ISS)
positive regulation of branching involved in ureteric bud morphogenesis  (ISO,ISS)
positive regulation of DNA-templated transcription  (ISO,ISS)
positive regulation of embryonic development  (ISO,ISS)
positive regulation of gastrulation  (ISO,ISS)
positive regulation of nephron tubule epithelial cell differentiation  (ISO,ISS)
post-embryonic development  (ISO,ISS)
primitive streak formation  (ISO,ISS)
pronephros development  (ISO)
regulation of gene expression  (ISO,ISS)
regulation of transcription by RNA polymerase II  (IBA)
renal vesicle morphogenesis  (ISO,ISS)
retina development in camera-type eye  (ISO)
retina layer formation  (ISO,ISS)
S-shaped body morphogenesis  (ISO,ISS)
somite rostral/caudal axis specification  (ISO)
spinal cord association neuron differentiation  (ISO,ISS)
spinal cord development  (ISO)
telencephalon development  (ISO)
transcription by RNA polymerase II  (ISO,ISS)
ureter morphogenesis  (ISO)
ureteric bud development  (ISO,ISS)
urogenital system development  (ISO,ISS)
uterine epithelium development  (ISO,ISS)
uterus development  (ISO,ISS)
vagina development  (ISO,ISS)
ventral spinal cord development  (ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Distribution of Rlim, an LIM homeodomain gene, in the rat brain. Furuyama T, etal., Neurosci Lett 1994 Apr 11;170(2):266-8.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. The LIM homeodomain protein Lim-1 is widely expressed in neural, neural crest and mesoderm derivatives in vertebrate development. Karavanov AA, etal., Int J Dev Biol. 1996 Apr;40(2):453-61.
5. Expression pattern of the rat Lim-1 homeobox gene suggests a dual role during kidney development. Karavanov AA, etal., Int J Dev Biol. 1998 Jan;42(1):61-6.
6. Gene Data Set MGD Curation, June 12, 2002
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7909549   PMID:10328927   PMID:10482234   PMID:10498685   PMID:10529425   PMID:10741426   PMID:11291865   PMID:14695376   PMID:15355796   PMID:15857913   PMID:15930111   PMID:16216236  
PMID:17166926   PMID:17610272   PMID:17664423   PMID:18076286   PMID:18094249   PMID:20711475   PMID:21731775   PMID:26494787  


Genomics

Comparative Map Data
Lhx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21069,396,829 - 69,403,617 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1069,396,829 - 69,403,617 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1074,016,816 - 74,023,604 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01073,521,849 - 73,528,637 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01068,986,264 - 68,993,052 (-)NCBIRnor_WKY
Rnor_6.01071,843,991 - 71,849,293 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1071,843,991 - 71,849,293 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01071,752,917 - 71,758,219 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41072,800,497 - 72,805,799 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11072,814,866 - 72,820,169 (-)NCBI
Celera1068,324,814 - 68,330,116 (-)NCBICelera
Cytogenetic Map10q26NCBI
LHX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381736,936,785 - 36,944,612 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1736,936,785 - 36,944,612 (+)EnsemblGRCh38hg38GRCh38
GRCh371735,294,772 - 35,301,912 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361732,368,612 - 32,374,607 (+)NCBINCBI36Build 36hg18NCBI36
Build 341732,368,611 - 32,374,607NCBI
Celera1732,116,628 - 32,122,623 (+)NCBICelera
Cytogenetic Map17q12NCBI
HuRef1731,230,715 - 31,237,858 (+)NCBIHuRef
CHM1_11735,329,038 - 35,336,178 (+)NCBICHM1_1
T2T-CHM13v2.01737,924,529 - 37,931,669 (+)NCBIT2T-CHM13v2.0
Lhx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391184,408,801 - 84,416,360 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1184,409,110 - 84,416,361 (-)EnsemblGRCm39 Ensembl
GRCm381184,517,975 - 84,525,534 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1184,518,284 - 84,525,535 (-)EnsemblGRCm38mm10GRCm38
MGSCv371184,332,881 - 84,339,036 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361184,335,574 - 84,341,729 (-)NCBIMGSCv36mm8
Celera1194,132,193 - 94,138,348 (-)NCBICelera
Cytogenetic Map11CNCBI
cM Map1151.31NCBI
Lhx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554511,037,825 - 1,048,501 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554511,037,936 - 1,048,501 (-)NCBIChiLan1.0ChiLan1.0
LHX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11720,430,618 - 20,437,751 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1720,430,618 - 20,437,751 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01720,134,308 - 20,140,652 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LHX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1936,760,890 - 36,768,345 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl936,761,826 - 36,768,164 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha935,986,818 - 35,993,342 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0937,571,199 - 37,577,732 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl937,571,878 - 37,576,839 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1936,353,003 - 36,359,535 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0936,640,659 - 36,647,196 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0936,727,884 - 36,734,417 (+)NCBIUU_Cfam_GSD_1.0
Lhx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560235,742,907 - 35,750,671 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364901,324,370 - 1,331,505 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364901,324,378 - 1,332,177 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1238,450,708 - 38,456,139 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11238,450,708 - 38,457,583 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21240,067,286 - 40,073,812 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LHX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11630,843,062 - 30,850,182 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1630,842,652 - 30,849,465 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660771,575,851 - 1,584,088 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lhx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248713,954,504 - 3,963,033 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248713,954,490 - 3,961,861 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lhx1
20 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:33
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000003799
Prediction methods: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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106134527681714865Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106134541382564856Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2298481Eau9Experimental allergic uveoretinitis QTL 90.0169uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)106592723382565079Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
631565Hcuc4Hepatic copper content QTL 44.15liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)106694181373452992Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
2289985Bp305Blood pressure QTL 305arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106750210873579767Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat

Markers in Region
D10Rat90  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21069,399,363 - 69,399,614 (+)MAPPERmRatBN7.2
Rnor_6.01071,845,040 - 71,845,290NCBIRnor6.0
Rnor_5.01071,753,966 - 71,754,216UniSTSRnor5.0
RGSC_v3.41072,801,535 - 72,801,883RGDRGSC3.4
RGSC_v3.41072,801,546 - 72,801,796UniSTSRGSC3.4
RGSC_v3.11072,815,905 - 72,816,253RGD
Celera1068,325,863 - 68,326,113UniSTS
RH 2.0 Map10713.5RGD
FHH x ACI Map1058.1099RGD
Cytogenetic Map10q26UniSTS


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 hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 31 20 6
Low 39 15 22
Below cutoff 2 9 9 9 2 2 2 8 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003799   ⟹   ENSRNOP00000003799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1069,396,829 - 69,403,617 (-)Ensembl
Rnor_6.0 Ensembl1071,843,991 - 71,849,293 (-)Ensembl
RefSeq Acc Id: NM_145880   ⟹   NP_665887
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21069,396,829 - 69,403,617 (-)NCBI
Rnor_6.01071,843,991 - 71,849,293 (-)NCBI
Rnor_5.01071,752,917 - 71,758,219 (-)NCBI
RGSC_v3.41072,800,497 - 72,805,799 (-)RGD
Celera1068,324,814 - 68,330,116 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_665887 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC60696 (Get FASTA)   NCBI Sequence Viewer  
  EDM05516 (Get FASTA)   NCBI Sequence Viewer  
  P63007 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_665887   ⟸   NM_145880
- UniProtKB: P63007 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003799   ⟸   ENSRNOT00000003799
Protein Domains
LIM zinc-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P63007-F1-model_v2 AlphaFold P63007 1-406 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71074 AgrOrtholog
BioCyc Gene G2FUF-23841 BioCyc
Ensembl Genes ENSRNOG00000002812 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003799 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003799 ENTREZGENE, UniProtKB/Swiss-Prot
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:257634 UniProtKB/Swiss-Prot
NCBI Gene 257634 ENTREZGENE
Pfam Homeodomain UniProtKB/Swiss-Prot
  LIM UniProtKB/Swiss-Prot
PhenoGen Lhx1 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 LHX1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P36199 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-30 Lhx1  LIM homeobox 1  Lhx1  LIM homeobox protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Lhx1  LIM homeobox protein 1      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in Purkinje cell layer of the cerebellum and nuclei of the hypothalamusmidbrainand pons 70776