LHX3 (LIM homeobox 3) - Rat Genome Database

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Gene: LHX3 (LIM homeobox 3) Canis lupus familiaris
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Symbol: LHX3
Name: LIM homeobox 3
RGD ID: 12128191
Description: ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN apoptotic process (ortholog); dorsal/ventral pattern formation (ortholog); lung development (ortholog); ASSOCIATED WITH Adams-Oliver Syndrome 5 (ortholog); amenorrhea (ortholog); atrial fibrillation (ortholog); FOUND IN chromatin (inferred); nucleus (inferred); transcription regulator complex (inferred)
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LIM homeodomain box protein 3; LIM/homeobox protein Lhx3
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,499,054 - 48,504,456 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0950,125,225 - 50,131,690 (+)NCBIROS_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_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References
Additional References at PubMed
PMID:22132174   PMID:22301074   PMID:25273400   PMID:25586673   PMID:30032202   PMID:33890524  


Genomics

Comparative Map Data
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,499,054 - 48,504,456 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0950,125,225 - 50,131,690 (+)NCBIROS_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_1.0
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 (-)EnsemblGRCh38hg38GRCh38
GRCh379139,088,096 - 139,096,974 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369138,227,917 - 138,236,776 (-)NCBINCBI36Build 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 Ensembl
GRCm38226,200,212 - 26,208,249 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,200,212 - 26,208,289 (-)EnsemblGRCm38mm10GRCm38
MGSCv37226,055,732 - 26,062,076 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36226,022,956 - 26,030,258 (-)NCBIMGSCv36mm8
Celera225,922,727 - 25,929,069 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map218.44NCBI
Lhx3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,424,620 - 29,432,637 (-)NCBIGRCr8
mRatBN7.239,026,432 - 9,035,122 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,027,425 - 9,034,480 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.033,653,861 - 3,662,509 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,654,755 - 3,661,810 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.039,015,656 - 9,023,734 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,381,890 - 4,389,132 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.134,387,210 - 4,387,304 (-)NCBI
Celera33,849,012 - 3,855,303 (-)NCBICelera
Cytogenetic Map3p13NCBI
Lhx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,464,149 - 4,470,962 (+)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247601,428,496 - 1,435,414 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LHX3
72 total Variants

Expression

RNA-SEQ Expression

adipose tissue
circulatory system
ectoderm
endocrine system
hemolymphoid system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
1 1 13 10 3 1 11 11 8 14

Sequence


Ensembl Acc Id: ENSCAFT00000020228   ⟹   ENSCAFP00000018765
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl949,248,621 - 49,254,118 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845012496   ⟹   ENSCAFP00845009762
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl950,125,225 - 50,130,622 (+)Ensembl
RefSeq Acc Id: NM_001197187   ⟹   NP_001184116
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1949,248,621 - 49,254,128 (+)NCBI
Dog10K_Boxer_Tasha948,499,054 - 48,504,456 (+)NCBI
ROS_Cfam_1.0950,125,225 - 50,130,622 (+)NCBI
UMICH_Zoey_3.1948,905,665 - 48,911,059 (+)NCBI
UNSW_CanFamBas_1.0949,199,965 - 49,205,359 (+)NCBI
UU_Cfam_GSD_1.0949,247,527 - 49,252,929 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038675092   ⟹   XP_038531020
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0950,126,164 - 50,131,690 (+)NCBI
RefSeq Acc Id: NP_001184116   ⟸   NM_001197187
- UniProtKB: E0X4D7 (UniProtKB/TrEMBL),   A0A8C0JKM2 (UniProtKB/TrEMBL),   A0A8C0LY98 (UniProtKB/TrEMBL),   A0A8C0T2C1 (UniProtKB/TrEMBL),   A0A8I3MU49 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCAFP00000018765   ⟸   ENSCAFT00000020228
RefSeq Acc Id: XP_038531020   ⟸   XM_038675092
- Peptide Label: isoform X1
- UniProtKB: A0A8C0JNR2 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845009762   ⟸   ENSCAFT00845012496
Protein Domains
Homeobox   LIM zinc-binding


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000019695 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030002147 UniProtKB/TrEMBL
  ENSCAFG00040017819 UniProtKB/TrEMBL
  ENSCAFG00845007030 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000020228.5 UniProtKB/TrEMBL
  ENSCAFT00030003934.1 UniProtKB/TrEMBL
  ENSCAFT00040032941.1 UniProtKB/TrEMBL
  ENSCAFT00845012496 ENTREZGENE
  ENSCAFT00845012496.1 UniProtKB/TrEMBL
Gene3D-CATH Cysteine Rich Protein UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  Lhx3/4-like_LIM2 UniProtKB/TrEMBL
  Lhx3_LIM1 UniProtKB/TrEMBL
  LIM_Homeobox_TF UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report cfa:607584 UniProtKB/TrEMBL
NCBI Gene LHX3 ENTREZGENE
PANTHER LIM/HOMEOBOX PROTEIN LHX UniProtKB/TrEMBL
  LIM/HOMEOBOX PROTEIN LHX3 UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
  LIM UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
  SSF46689 UniProtKB/TrEMBL
UniProt A0A8C0JKM2 ENTREZGENE
  A0A8C0JNR2 ENTREZGENE
  A0A8C0LY98 ENTREZGENE
  A0A8C0T2C1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3MU49 ENTREZGENE, UniProtKB/TrEMBL
  E0X4D6_CANLF UniProtKB/TrEMBL
  E0X4D7 ENTREZGENE, UniProtKB/TrEMBL
  G3BKG0_CANLF UniProtKB/TrEMBL
UniProt Secondary A0A8C0LY98 UniProtKB/TrEMBL
VGNC ID VGNC:42664 ENTREZGENE