LHX1 (LIM homeobox 1) - Rat Genome Database

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Gene: LHX1 (LIM homeobox 1) Canis lupus familiaris
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Symbol: LHX1
Name: LIM homeobox 1
RGD ID: 12325752
Description: ENCODES a protein that exhibits DNA-binding transcription factor activity (ortholog); sequence-specific double-stranded DNA binding (ortholog); INVOLVED IN anatomical structure formation involved in morphogenesis (ortholog); anatomical structure morphogenesis (ortholog); anterior/posterior axis specification (ortholog); ASSOCIATED WITH autism spectrum disorder (ortholog); autistic disorder (ortholog); chromosome 17q12 deletion syndrome (ortholog); FOUND IN nucleus (ortholog); protein-containing complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Also known as: LIM/homeobox protein Lhx1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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 (+)NCBI
ROS_Cfam_1.0937,571,199 - 37,577,732 (+)NCBI
UMICH_Zoey_3.1936,353,003 - 36,359,535 (+)NCBI
UNSW_CanFamBas_1.0936,640,659 - 36,647,196 (+)NCBI
UU_Cfam_GSD_1.0936,727,884 - 36,734,417 (+)NCBI
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  (IEA,ISO)
cell differentiation  (ISO)
cell-cell signaling  (ISO,ISS)
cellular response to fibroblast growth factor stimulus  (ISO)
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  (ISS)
comma-shaped body morphogenesis  (ISS)
dorsal spinal cord interneuron posterior axon guidance  (ISS)
dorsal/ventral pattern formation  (ISO,ISS)
ectoderm formation  (ISO,ISS)
embryonic pattern specification  (ISO,ISS)
embryonic retina morphogenesis in camera-type eye  (ISS)
embryonic viscerocranium morphogenesis  (ISS)
endoderm development  (ISO)
endoderm formation  (ISO,ISS)
epithelium development  (ISS)
forebrain regionalization  (ISO,ISS)
gastrulation with mouth forming second  (ISO,ISS)
head development  (ISO,ISS)
horizontal cell localization  (IEA)
kidney development  (ISO,ISS)
lateral motor column neuron migration  (ISS)
mesendoderm development  (IEA,ISO)
mesonephric duct development  (ISO)
mesonephric tubule development  (ISO)
mesonephros development  (ISO)
metanephric comma-shaped body morphogenesis  (ISO)
metanephric glomerulus development  (ISO)
metanephric part of ureteric bud development  (ISO)
metanephric renal vesicle morphogenesis  (IEA,ISO)
metanephric S-shaped body morphogenesis  (IEA,ISO)
metanephros development  (ISO)
motor neuron axon guidance  (ISS)
negative regulation of transcription, DNA-templated  (ISS)
nephric duct elongation  (IEA)
nephric duct morphogenesis  (ISS)
neuron differentiation  (IBA)
oviduct development  (ISS)
oviduct epithelium development  (ISS)
paramesonephric duct development  (ISS)
pattern specification process  (ISO,ISS)
positive regulation of anterior head development  (ISS)
positive regulation of branching involved in ureteric bud morphogenesis  (ISS)
positive regulation of embryonic development  (ISS)
positive regulation of gastrulation  (ISS)
positive regulation of nephron tubule epithelial cell differentiation  (ISS)
positive regulation of transcription, DNA-templated  (ISS)
post-embryonic development  (ISO,ISS)
primitive streak formation  (ISO,ISS)
pronephros development  (IEA,ISO)
regulation of gene expression  (ISO,ISS)
regulation of transcription by RNA polymerase II  (IBA)
renal vesicle morphogenesis  (ISS)
retina development in camera-type eye  (ISO)
retina layer formation  (ISO,ISS)
S-shaped body morphogenesis  (ISS)
somite rostral/caudal axis specification  (IEA,ISO)
spinal cord association neuron differentiation  (ISS)
spinal cord development  (ISO)
telencephalon development  (IEA,ISO)
transcription by RNA polymerase II  (ISS)
ureter morphogenesis  (IEA,ISO)
ureteric bud development  (ISO,ISS)
urogenital system development  (ISO,ISS)
uterine epithelium development  (ISS)
uterus development  (ISS)
vagina development  (ISS)
ventral spinal cord development  (IEA,ISO)

Cellular Component

References

Genomics

Comparative Map Data
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 (+)NCBI
ROS_Cfam_1.0937,571,199 - 37,577,732 (+)NCBI
UMICH_Zoey_3.1936,353,003 - 36,359,535 (+)NCBI
UNSW_CanFamBas_1.0936,640,659 - 36,647,196 (+)NCBI
UU_Cfam_GSD_1.0936,727,884 - 36,734,417 (+)NCBI
LHX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1736,936,785 - 36,944,612 (+)EnsemblGRCh38hg38GRCh38
GRCh381736,937,475 - 36,944,612 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371735,294,772 - 35,301,912 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361732,368,612 - 32,374,607 (+)NCBINCBI36hg18NCBI36
Build 341732,368,611 - 32,374,607NCBI
Celera1732,116,628 - 32,122,623 (+)NCBI
Cytogenetic Map17q12NCBI
HuRef1731,230,715 - 31,237,858 (+)NCBIHuRef
CHM1_11735,329,038 - 35,336,178 (+)NCBICHM1_1
Lhx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391184,408,801 - 84,416,360 (-)NCBIGRCm39mm39
GRCm39 Ensembl1184,409,110 - 84,416,361 (-)Ensembl
GRCm381184,517,975 - 84,525,534 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1184,518,284 - 84,525,535 (-)EnsemblGRCm38mm10GRCm38
MGSCv371184,332,881 - 84,339,036 (-)NCBIGRCm37mm9NCBIm37
MGSCv361184,335,574 - 84,341,729 (-)NCBImm8
Celera1194,132,193 - 94,138,348 (-)NCBICelera
Cytogenetic Map11CNCBI
cM Map1151.31NCBI
Lhx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21069,396,829 - 69,403,617 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1069,396,829 - 69,403,617 (-)Ensembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11072,814,866 - 72,820,169 (-)NCBI
Celera1068,324,814 - 68,330,116 (-)NCBICelera
Cytogenetic Map10q26NCBI
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_v0panPan3
Lhx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560235,742,907 - 35,750,671 (+)NCBI
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 (-)NCBI
ChlSab1.1 Ensembl1630,842,652 - 30,849,465 (-)Ensembl
Vero_WHO_p1.0NW_0236660771,575,851 - 1,584,088 (-)NCBI
Lhx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248713,954,490 - 3,961,861 (+)NCBI


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

alimentary part of gastrointestinal system endocrine system exocrine system hepatobiliary system nervous system reproductive system respiratory system adipose tissue
High
Medium
Low 1 1
Below cutoff 1 6 1 1 7 8 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000028326   ⟹   ENSCAFP00000026343
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl936,761,826 - 36,768,164 (+)Ensembl
RefSeq Acc Id: XM_014116734   ⟹   XP_013972209
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1936,760,890 - 36,768,345 (+)NCBI
Dog10K_Boxer_Tasha935,986,818 - 35,993,342 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038486209   ⟹   XP_038342137
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1936,353,003 - 36,359,535 (+)NCBI
RefSeq Acc Id: XM_038548027   ⟹   XP_038403955
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0936,727,884 - 36,734,417 (+)NCBI
RefSeq Acc Id: XM_038611995   ⟹   XP_038467923
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0936,640,659 - 36,647,196 (+)NCBI
RefSeq Acc Id: XM_038677241   ⟹   XP_038533169
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0937,571,199 - 37,577,732 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_013972209   ⟸   XM_014116734
- UniProtKB: E2RMA8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000026343   ⟸   ENSCAFT00000028326
RefSeq Acc Id: XP_038342137   ⟸   XM_038486209
RefSeq Acc Id: XP_038467923   ⟸   XM_038611995
RefSeq Acc Id: XP_038533169   ⟸   XM_038677241
RefSeq Acc Id: XP_038403955   ⟸   XM_038548027


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000017853 Ensembl, ENTREZGENE
Ensembl Protein ENSCAFP00000026343 ENTREZGENE
NCBI Gene LHX1 ENTREZGENE
UniProt E2RMA8 ENTREZGENE
VGNC ID VGNC:42662 ENTREZGENE