Lhx1 (LIM homeobox 1) - Rat Genome Database

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Gene: Lhx1 (LIM homeobox 1) Ictidomys tridecemlineatus
Analyze
Symbol: Lhx1
Name: LIM homeobox 1
RGD ID: 12522039
Description: ENCODES a protein that exhibits cis-regulatory region sequence-specific DNA binding (inferred); DNA binding (inferred); DNA-binding transcription factor activity (inferred); 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 (inferred); protein-containing complex (inferred); transcription regulator complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LIM/homeobox protein Lhx1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364901,324,378 - 1,332,177 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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  (IEA,ISO)
anatomical structure morphogenesis  (IEA,ISO)
anterior/posterior axis specification  (IEA,ISO)
anterior/posterior pattern specification  (IEA,ISO)
branching involved in ureteric bud morphogenesis  (IEA)
cell differentiation  (IEA,ISO)
cell-cell signaling  (IEA,ISO)
cellular response to fibroblast growth factor stimulus  (ISO)
cerebellar Purkinje cell differentiation  (IEA,ISO)
cerebellar Purkinje cell-granule cell precursor cell signaling  (IEA,ISO)
cerebellum development  (IEA,ISO)
cervix development  (IEA)
comma-shaped body morphogenesis  (IEA)
dorsal/ventral pattern formation  (IEA,ISO)
ectoderm formation  (IEA,ISO)
embryonic pattern specification  (IEA,ISO)
embryonic retina morphogenesis in camera-type eye  (IEA)
embryonic viscerocranium morphogenesis  (IEA)
endoderm development  (IEA,ISO)
endoderm formation  (IEA,ISO)
epithelium development  (IEA)
forebrain regionalization  (IEA,ISO)
gastrulation with mouth forming second  (IEA,ISO)
head development  (IEA,ISO)
kidney development  (IEA,ISO)
lateral motor column neuron migration  (IEA)
mesendoderm development  (IEA,ISO)
mesonephric duct development  (ISO)
mesonephric tubule development  (ISO)
mesonephros development  (IEA)
metanephric comma-shaped body morphogenesis  (ISO)
metanephric glomerulus development  (ISO)
metanephric part of ureteric bud development  (ISO)
metanephric renal vesicle morphogenesis  (IEA)
metanephric S-shaped body morphogenesis  (IEA)
metanephros development  (IEA)
motor neuron axon guidance  (IEA)
negative regulation of DNA-templated transcription  (IEA)
nephric duct elongation  (IEA)
nephric duct morphogenesis  (IEA)
neuron differentiation  (IEA)
oviduct development  (IEA)
oviduct epithelium development  (IEA)
paramesonephric duct development  (IEA)
pattern specification process  (IEA,ISO)
positive regulation of anterior head development  (IEA)
positive regulation of branching involved in ureteric bud morphogenesis  (IEA)
positive regulation of DNA-templated transcription  (IEA)
positive regulation of embryonic development  (IEA)
positive regulation of gastrulation  (IEA)
positive regulation of nephron tubule epithelial cell differentiation  (IEA)
post-embryonic development  (IEA,ISO)
primitive streak formation  (IEA,ISO)
pronephros development  (IEA)
regulation of DNA-templated transcription  (IEA)
regulation of gene expression  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IEA)
renal vesicle morphogenesis  (IEA)
retina development in camera-type eye  (IEA)
retina layer formation  (IEA)
S-shaped body morphogenesis  (IEA)
somite rostral/caudal axis specification  (IEA,ISO)
spinal cord association neuron differentiation  (IEA)
spinal cord development  (IEA)
system development  (IEA)
telencephalon development  (IEA)
transcription by RNA polymerase II  (IEA)
ureter morphogenesis  (IEA,ISO)
ureteric bud development  (IEA,ISO)
urogenital system development  (IEA,ISO)
uterine epithelium development  (IEA)
uterus development  (IEA)
vagina development  (IEA)
ventral spinal cord development  (IEA)

Cellular Component

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364901,324,378 - 1,332,177 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381736,936,785 - 36,944,612 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 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-CHM13v2.01737,923,784 - 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81069,894,288 - 69,901,076 (-)NCBIGRCr8
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_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01073,521,849 - 73,528,637 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01068,986,264 - 68,993,052 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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
(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
NHGRI_mPanPan1-v21927,813,531 - 27,819,154 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11729,695,186 - 29,700,812 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01720,134,308 - 20,140,652 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11720,430,618 - 20,437,751 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1720,430,618 - 20,437,751 (-)Ensemblpanpan1.1panPan2
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
(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


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSSTOT00000024382   ⟹   ENSSTOP00000017354
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049364901,324,370 - 1,331,505 (-)Ensembl
RefSeq Acc Id: XM_005321524   ⟹   XP_005321581
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560235,742,907 - 35,750,671 (+)NCBI
SpeTri2.0NW_0049364901,324,378 - 1,332,177 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040269108   ⟹   XP_040125042
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560235,745,844 - 35,750,671 (+)NCBI
Protein Sequences
Protein RefSeqs XP_005321581 (Get FASTA)   NCBI Sequence Viewer  
  XP_040125042 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000017354.1
GenBank Protein KAG3269433 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_005321581   ⟸   XM_005321524
- Peptide Label: isoform X2
- UniProtKB: I3MZ08 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040125042   ⟸   XM_040269108
- Peptide Label: isoform X1
Ensembl Acc Id: ENSSTOP00000017354   ⟸   ENSSTOT00000024382
Protein Domains
Homeobox   LIM zinc-binding


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000022593 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000024382.2 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
  Lhx1/5_LIM1 UniProtKB/TrEMBL
  Lhx1/5_LIM2 UniProtKB/TrEMBL
  LIM_Homeobox_TF UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
NCBI Gene Lhx1 ENTREZGENE
PANTHER LIM/HOMEOBOX PROTEIN LHX UniProtKB/TrEMBL
  LIM/HOMEOBOX PROTEIN LHX1 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 I3MZ08 ENTREZGENE, UniProtKB/TrEMBL