LHX1 (LIM homeobox 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: LHX1 (LIM homeobox 1) Sus scrofa
Analyze
Symbol: LHX1
Name: LIM homeobox 1
RGD ID: 14081911
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 protein-containing complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Also known as: LIM/homeobox protein Lhx1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
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)
anatomical structure morphogenesis  (ISO)
anterior/posterior axis specification  (ISO)
anterior/posterior pattern specification  (ISO)
branching involved in ureteric bud morphogenesis  (IEA,ISO)
cell differentiation  (ISO)
cell-cell signaling  (ISO)
cellular response to fibroblast growth factor stimulus  (ISO)
cerebellar Purkinje cell differentiation  (IEA,ISO)
cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation  (IEA,ISO)
cerebellum development  (ISO)
cervix development  (IEA)
comma-shaped body morphogenesis  (IEA)
dorsal/ventral pattern formation  (IEA,ISO)
ectoderm formation  (IEA,ISO)
embryonic pattern specification  (ISO)
embryonic retina morphogenesis in camera-type eye  (IEA)
embryonic viscerocranium morphogenesis  (IEA)
endoderm development  (ISO)
endoderm formation  (IEA,ISO)
epithelium development  (ISO)
forebrain regionalization  (IEA,ISO)
gastrulation with mouth forming second  (ISO)
head development  (ISO)
horizontal cell localization  (IEA)
kidney development  (ISO)
lateral motor column neuron migration  (IEA)
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  (IEA)
negative regulation of transcription, DNA-templated  (IEA)
nephric duct elongation  (IEA)
nephric duct morphogenesis  (ISO)
neuron differentiation  (IBA)
oviduct development  (ISO)
oviduct epithelium development  (ISO)
paramesonephric duct development  (IEA)
pattern specification process  (ISO)
positive regulation of anterior head development  (IEA)
positive regulation of branching involved in ureteric bud morphogenesis  (IEA)
positive regulation of embryonic development  (ISO)
positive regulation of gastrulation  (IEA)
positive regulation of nephron tubule epithelial cell differentiation  (IEA)
positive regulation of transcription, DNA-templated  (IEA)
post-embryonic development  (IEA,ISO)
primitive streak formation  (IEA,ISO)
pronephros development  (IEA,ISO)
regulation of gene expression  (ISO)
regulation of transcription by RNA polymerase II  (IBA,IEA)
renal vesicle morphogenesis  (ISO)
retina development in camera-type eye  (ISO)
retina layer formation  (ISO)
S-shaped body morphogenesis  (ISO)
somite rostral/caudal axis specification  (IEA,ISO)
spinal cord association neuron differentiation  (IEA)
spinal cord development  (ISO)
telencephalon development  (IEA,ISO)
transcription by RNA polymerase II  (IEA)
ureter morphogenesis  (IEA,ISO)
ureteric bud development  (ISO)
urogenital system development  (ISO)
uterine epithelium development  (IEA)
uterus development  (ISO)
vagina development  (IEA)
ventral spinal cord development  (IEA,ISO)

Cellular Component

References

Genomics

Comparative Map Data
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
(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
(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
(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
(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 nervous system renal system reproductive system
High
Medium
Low 10 2
Below cutoff 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000019256   ⟹   ENSSSCP00000018746
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1238,450,708 - 38,456,139 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000063575   ⟹   ENSSSCP00000031751
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1238,450,708 - 38,456,139 (+)Ensembl
RefSeq Acc Id: XM_003131706   ⟹   XP_003131754
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11238,450,708 - 38,457,583 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003131754 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_003131754   ⟸   XM_003131706
- UniProtKB: F2Z531 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000018746   ⟸   ENSSSCT00000019256
RefSeq Acc Id: ENSSSCP00000031751   ⟸   ENSSSCT00000063575
Protein Domains
Homeobox   LIM zinc-binding


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000017692 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00070004970 UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000018746 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00000031751 UniProtKB/TrEMBL
  ENSSSCP00070007717 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000019256 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00000063575 UniProtKB/TrEMBL
  ENSSSCT00070009418 UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report ssc:100513681 UniProtKB/TrEMBL
NCBI Gene LHX1 ENTREZGENE
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 SSF46689 UniProtKB/TrEMBL
UniProt A0A286ZJJ7_PIG UniProtKB/TrEMBL
  A0A4X1SZB4_PIG UniProtKB/TrEMBL
  F2Z531 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:89711 ENTREZGENE