Lhx3 (LIM homeobox 3) - Rat Genome Database

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Gene: Lhx3 (LIM homeobox 3) Rattus norvegicus
Analyze
Symbol: Lhx3
Name: LIM homeobox 3
RGD ID: 71078
Description: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and transcription coactivator binding activity. Involved in lung development. Predicted to be located in chromatin. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in combined pituitary hormone deficiency 3. Orthologous to human LHX3 (LIM homeobox 3); INTERACTS WITH bisphenol A; C60 fullerene; cefaloridine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LIM homeobox protein 3; LIM homeodomain protein 3a; LIM/homeobox protein Lhx3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,424,620 - 29,432,637 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl329,424,620 - 29,432,637 (-)EnsemblGRCr8
mRatBN7.239,026,432 - 9,035,122 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,027,425 - 9,034,480 (-)EnsemblmRatBN7.2
Rnor_6.033,653,861 - 3,662,509 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,654,755 - 3,661,810 (-)Ensemblrn6Rnor6.0
Rnor_5.039,015,656 - 9,023,734 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.434,381,890 - 4,389,132 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera33,849,012 - 3,855,303 (-)NCBICelera
RGSC_v3.134,387,210 - 4,387,304 (-)NCBI
Cytogenetic Map3p13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IEA,ISO)
nucleus  (IBA,IEA,ISO)
transcription regulator complex  (IEA,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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Gene Data Set MGD Curation, June 12, 2002
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. An isoform-specific inhibitory domain regulates the LHX3 LIM homeodomain factor holoprotein and the production of a functional alternate translation form. Sloop KW, etal., J Biol Chem 2001 Sep 28;276(39):36311-9.
11. Gene expression profiling identifies regulatory pathways involved in the late stage of rat fetal lung development. Weng T, etal., Am J Physiol Lung Cell Mol Physiol. 2006 Nov;291(5):L1027-37. Epub 2006 Jun 23.
Additional References at PubMed
PMID:8638120   PMID:9192866   PMID:9207461   PMID:9865699   PMID:10195693   PMID:10431247   PMID:10482234   PMID:10593900   PMID:15271874   PMID:18037398   PMID:18407919   PMID:18425848  
PMID:19323994   PMID:19666821   PMID:26612202  


Genomics

Comparative Map Data
Lhx3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,424,620 - 29,432,637 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl329,424,620 - 29,432,637 (-)EnsemblGRCr8
mRatBN7.239,026,432 - 9,035,122 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,027,425 - 9,034,480 (-)EnsemblmRatBN7.2
Rnor_6.033,653,861 - 3,662,509 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,654,755 - 3,661,810 (-)Ensemblrn6Rnor6.0
Rnor_5.039,015,656 - 9,023,734 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.434,381,890 - 4,389,132 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera33,849,012 - 3,855,303 (-)NCBICelera
RGSC_v3.134,387,210 - 4,387,304 (-)NCBI
Cytogenetic Map3p13NCBI
LHX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389136,196,250 - 136,205,128 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,196,250 - 136,205,128 (-)Ensemblhg38GRCh38
GRCh379139,088,096 - 139,096,974 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369138,227,917 - 138,236,776 (-)NCBIBuild 36Build 36hg18NCBI36
Build 349136,314,040 - 136,322,900NCBI
Celera9109,606,466 - 109,615,325 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9108,552,281 - 108,560,958 (-)NCBIHuRef
CHM1_19139,236,859 - 139,245,718 (-)NCBICHM1_1
T2T-CHM13v2.09148,425,793 - 148,434,671 (-)NCBIT2T-CHM13v2.0
Lhx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,090,224 - 26,098,261 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl226,090,224 - 26,098,301 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38226,200,212 - 26,208,249 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,200,212 - 26,208,289 (-)Ensemblmm10GRCm38
MGSCv37226,055,732 - 26,062,076 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36226,022,956 - 26,030,258 (-)NCBIMGSCv36mm8
Celera225,922,727 - 25,929,069 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map218.44NCBI
Lhx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,464,149 - 4,470,962 (+)Ensembl
ChiLan1.0NW_0049555134,464,149 - 4,470,962 (+)NCBIChiLan1.0ChiLan1.0
LHX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2113,179,178 - 3,188,054 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan193,181,513 - 3,190,389 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09107,271,131 - 107,280,001 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19136,252,974 - 136,260,366 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9136,252,880 - 136,260,366 (-)EnsemblpanPan2panpan1.1
LHX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,248,555 - 49,254,128 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,248,621 - 49,254,118 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha948,499,054 - 48,504,456 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0950,125,225 - 50,131,690 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,125,225 - 50,130,622 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,905,665 - 48,911,059 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,199,965 - 49,205,359 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,247,527 - 49,252,929 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lhx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947201,802,058 - 201,811,080 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366691,564,102 - 1,573,047 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366691,561,433 - 1,573,074 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHX3
(Sus scrofa - pig)		 No map positions available.
LHX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,997,437 - 2,007,473 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl122,000,638 - 2,006,430 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660583,207,070 - 3,217,084 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lhx3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247601,429,384 - 1,435,414 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247601,428,496 - 1,435,414 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Lhx3
28 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:143
Count of miRNA genes:68
Interacting mature miRNAs:73
Transcripts:ENSRNOT00000025047, ENSRNOT00000045587
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3822719433703538Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
11 1 23 135 37 33 10 51 10 6 145 87 1 123 36 91 23 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000025047   ⟹   ENSRNOP00000025047
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl329,424,620 - 29,432,637 (-)Ensembl
mRatBN7.2 Ensembl39,027,425 - 9,034,480 (-)Ensembl
Rnor_6.0 Ensembl33,654,755 - 3,661,810 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000045587   ⟹   ENSRNOP00000044069
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl329,424,620 - 29,430,979 (-)Ensembl
mRatBN7.2 Ensembl39,027,425 - 9,032,676 (-)Ensembl
Rnor_6.0 Ensembl33,654,755 - 3,660,006 (-)Ensembl
RefSeq Acc Id: NM_001426997   ⟹   NP_001413926
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,424,620 - 29,432,637 (-)NCBI
RefSeq Acc Id: XM_039106128   ⟹   XP_038962056
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,424,623 - 29,430,891 (-)NCBI
mRatBN7.239,026,432 - 9,030,895 (-)NCBI
RefSeq Acc Id: XM_063283029   ⟹   XP_063139099
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,424,623 - 29,430,892 (-)NCBI
Ensembl Acc Id: ENSRNOP00000044069   ⟸   ENSRNOT00000045587
Ensembl Acc Id: ENSRNOP00000025047   ⟸   ENSRNOT00000025047
RefSeq Acc Id: XP_038962056   ⟸   XM_039106128
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001413926   ⟸   NM_001426997
- UniProtKB: A6JTC5 (UniProtKB/TrEMBL),   G3V8E3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139099   ⟸   XM_063283029
- Peptide Label: isoform X2
- UniProtKB: A6JTC6 (UniProtKB/TrEMBL),   G3V9E7 (UniProtKB/TrEMBL)
Protein Domains
Homeobox   LIM zinc-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V9E7-F1-model_v2 AlphaFold G3V9E7 1-402 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:71078 AgrOrtholog
BioCyc Gene G2FUF-50393 BioCyc
Ensembl Genes ENSRNOG00000018427 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025047 ENTREZGENE
  ENSRNOT00000025047.5 UniProtKB/TrEMBL
  ENSRNOT00000045587 ENTREZGENE
  ENSRNOT00000045587.2 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
  Lhx3/4-like_LIM2 UniProtKB/TrEMBL
  Lhx3_LIM1 UniProtKB/TrEMBL
  LIM_Homeobox_TF UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
NCBI Gene 170671 ENTREZGENE
PANTHER LIM/HOMEOBOX PROTEIN LHX UniProtKB/TrEMBL
  LIM/HOMEOBOX PROTEIN LHX3 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
PhenoGen Lhx3 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018427 RatGTEx
SMART HOX UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
  Homeodomain_like UniProtKB/TrEMBL
UniProt A6JTC5 ENTREZGENE, UniProtKB/TrEMBL
  A6JTC6 ENTREZGENE, UniProtKB/TrEMBL
  G3V8E3 ENTREZGENE, UniProtKB/TrEMBL
  G3V9E7 ENTREZGENE, UniProtKB/TrEMBL
  Q91ZX3_RAT UniProtKB/TrEMBL
  Q91ZX4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-26 Lhx3  LIM homeobox 3  Lhx3  LIM homeobox protein 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Lhx3  LIM homeobox protein 3      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein isoforms LXH3a and LXH3b have different N-terminal sequences 70778