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P63006 (LHX1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
LIM/homeobox protein Lhx1

Short name=LIM homeobox protein 1
Alternative name(s):
Homeobox protein Lim-1
Gene names
Name:Lhx1
Synonyms:Lim-1, Lim1
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length406 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis. Ref.2

Subunit structure

Interacts with LDB1 via the tandem LIM domains. Ref.5 Ref.6

Subcellular location

Nucleus Ref.4.

Tissue specificity

In mid to late stage embryos, expressed in a restricted region of mesoderm in the primitive streak. At 7.5 days, expressed in a horseshoe shape at the periphery of the node, as well as along both sides of the adjacent notochord. Also present in presumptive lateral and intermediate mesoderm. Later, expression become progressively restricted to intermediate mesoderm, and the developing excretory system including the pronephric region, mesonephros, nephric duct and metanephros. In the metanephros, strongly expressed in renal vesicles and S-shaped and coma-shaped bodies, as well as in the ureteric bud and its derivatives. Also expressed in the dorsal root ganglia. By stage 10.5, also expressed in regions of the central nervous system in the telencephalon through to the spinal cord. In adults, expressed in the cerebellum/medulla and kidney, and at very low levels in the cerebrum. Ref.1 Ref.2 Ref.4

Developmental stage

Expressed in both embryos and adults. Ref.1

Domain

The LIM domains exert a negative regulatory function and disruption of the LIM domains produces an activated form. In addition, two activation domains and a negative regulatory domain exist C-terminally to the homeobox By similarity.

Sequence similarities

Contains 1 homeobox DNA-binding domain.

Contains 2 LIM zinc-binding domains.

Ontologies

Keywords
   Biological processDifferentiation
Neurogenesis
Transcription
Transcription regulation
   Cellular componentNucleus
   DomainHomeobox
LIM domain
Repeat
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionDevelopmental protein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processS-shaped body morphogenesis

Inferred from mutant phenotype PubMed 17610272. Source: UniProtKB

anatomical structure formation involved in morphogenesis

Inferred from mutant phenotype PubMed 15930111. Source: MGI

anatomical structure morphogenesis

Inferred from mutant phenotype PubMed 10328927PubMed 15930111. Source: MGI

anterior/posterior axis specification

Inferred from genetic interaction PubMed 10529425. Source: MGI

anterior/posterior pattern specification

Inferred from genetic interaction PubMed 10498685. Source: MGI

branching involved in ureteric bud morphogenesis

Inferred from expression pattern PubMed 7909549. Source: UniProtKB

cell-cell signaling

Inferred from genetic interaction PubMed 17664423. Source: MGI

cellular response to fibroblast growth factor stimulus

Inferred from electronic annotation. Source: Ensembl

cerebellar Purkinje cell differentiation

Inferred from genetic interaction PubMed 17664423. Source: MGI

cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation

Inferred from genetic interaction PubMed 17664423. Source: MGI

cerebellum development

Inferred from genetic interaction PubMed 17664423. Source: MGI

cervix development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

comma-shaped body morphogenesis

Inferred from mutant phenotype PubMed 17610272. Source: UniProtKB

dorsal/ventral pattern formation

Inferred from genetic interaction PubMed 10498685. Source: MGI

ectoderm formation

Inferred from genetic interaction PubMed 10498685. Source: MGI

embryonic pattern specification

Inferred from genetic interaction PubMed 10529425. Source: MGI

embryonic retina morphogenesis in camera-type eye

Inferred from mutant phenotype PubMed 18094249. Source: UniProtKB

embryonic viscerocranium morphogenesis

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

endoderm formation

Inferred from mutant phenotype PubMed 15355796. Source: MGI

epithelium development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

forebrain regionalization

Inferred from genetic interaction PubMed 10529425. Source: MGI

gastrulation with mouth forming second

Inferred from mutant phenotype PubMed 15355796. Source: MGI

head development

Inferred from genetic interaction PubMed 15857913. Source: UniProtKB

horizontal cell localization

Inferred from mutant phenotype PubMed 18094249. Source: UniProtKB

kidney development

Inferred from mutant phenotype PubMed 15930111. Source: MGI

lateral motor column neuron migration

Inferred from mutant phenotype PubMed 20711475. Source: UniProtKB

mesonephric duct development

Inferred from electronic annotation. Source: Ensembl

mesonephros development

Inferred from expression pattern PubMed 7909549. Source: UniProtKB

metanephric S-shaped body morphogenesis

Inferred from expression pattern PubMed 7909549. Source: UniProtKB

metanephric comma-shaped body morphogenesis

Inferred from electronic annotation. Source: Ensembl

metanephric glomerulus development

Inferred from electronic annotation. Source: Ensembl

metanephric part of ureteric bud development

Inferred from electronic annotation. Source: Ensembl

metanephric renal vesicle morphogenesis

Inferred from expression pattern PubMed 7909549. Source: UniProtKB

metanephros development

Inferred from expression pattern PubMed 7909549. Source: UniProtKB

motor neuron axon guidance

Inferred from mutant phenotype PubMed 20711475. Source: UniProtKB

negative regulation of transcription, DNA-templated

Inferred from mutant phenotype PubMed 17610272. Source: UniProtKB

nephric duct elongation

Inferred from mutant phenotype PubMed 16216236. Source: UniProtKB

nephric duct morphogenesis

Inferred from mutant phenotype PubMed 16216236. Source: UniProtKB

oviduct development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

oviduct epithelium development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

paramesonephric duct development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

pattern specification process

Inferred from mutant phenotype PubMed 15930111. Source: MGI

positive regulation of anterior head development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

positive regulation of branching involved in ureteric bud morphogenesis

Inferred from mutant phenotype PubMed 16216236. Source: UniProtKB

positive regulation of embryonic development

Inferred from mutant phenotype PubMed 11291865. Source: UniProtKB

positive regulation of gastrulation

Inferred from mutant phenotype PubMed 11291865. Source: UniProtKB

positive regulation of nephron tubule epithelial cell differentiation

Inferred from mutant phenotype PubMed 16216236. Source: UniProtKB

positive regulation of transcription, DNA-templated

Inferred from mutant phenotype PubMed 11291865PubMed 16216236PubMed 17610272PubMed 20711475. Source: UniProtKB

post-embryonic development

Inferred from mutant phenotype PubMed 17664423. Source: MGI

primitive streak formation

Inferred from mutant phenotype PubMed 11291865. Source: UniProtKB

pronephros development

Inferred from expression pattern PubMed 7909549. Source: UniProtKB

regulation of gene expression

Inferred from mutant phenotype PubMed 10328927. Source: MGI

renal system development

Inferred from genetic interaction PubMed 21731775. Source: MGI

renal vesicle morphogenesis

Inferred from mutant phenotype PubMed 17610272. Source: UniProtKB

retina development in camera-type eye

Inferred from expression pattern PubMed 10741426. Source: UniProtKB

retina layer formation

Inferred from mutant phenotype PubMed 18094249. Source: UniProtKB

somite rostral/caudal axis specification

Inferred from mutant phenotype PubMed 11291865. Source: MGI

spinal cord association neuron differentiation

Inferred from genetic interaction PubMed 17166926. Source: UniProtKB

spinal cord development

Inferred from expression pattern PubMed 7909549. Source: UniProtKB

telencephalon development

Inferred from expression pattern PubMed 7909549. Source: UniProtKB

transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 15857913. Source: UniProtKB

ureteric bud development

Inferred from mutant phenotype PubMed 15930111. Source: MGI

urogenital system development

Inferred from mutant phenotype PubMed 15930111. Source: MGI

uterine epithelium development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

uterus development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

vagina development

Inferred from mutant phenotype PubMed 14695376. Source: UniProtKB

ventral spinal cord development

Inferred from expression pattern PubMed 20711475. Source: UniProtKB

   Cellular_componentintracellular

Inferred from direct assay PubMed 10482234. Source: MGI

nucleus

Inferred from direct assay PubMed 10741426PubMed 18094249Ref.4. Source: UniProtKB

protein complex

Inferred from direct assay PubMed 15857913. Source: UniProtKB

   Molecular_functionprotein binding

Inferred from physical interaction Ref.6. Source: UniProtKB

sequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from mutant phenotype PubMed 11291865PubMed 16216236PubMed 17610272PubMed 20711475. Source: UniProtKB

transcription corepressor activity

Inferred from sequence or structural similarity. Source: UniProtKB

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 406406LIM/homeobox protein Lhx1
PRO_0000075771

Regions

Domain4 – 5451LIM zinc-binding 1
Domain63 – 11755LIM zinc-binding 2
DNA binding180 – 23960Homeobox

Experimental info

Mutagenesis281C → G: Disrupts LDB1-binding; when associated with G-88. Ref.5
Mutagenesis881C → G: Disrupts LDB1-binding; when associated with G-28. Ref.5
Sequence conflict121L → LARQVRPVL Ref.2
Sequence conflict24 – 318Missing in AAC60669. Ref.2
Sequence conflict2361R → A in AAC60669. Ref.2
Sequence conflict3351H → HH in AAC60669. Ref.2

Sequences

Sequence LengthMass (Da)Tools
P63006 [UniParc].

Last modified August 31, 2004. Version 1.
Checksum: CC8637984998ADAF

FASTA40644,780
        10         20         30         40         50         60 
MVHCAGCKRP ILDRFLLNVL DRAWHVKCVQ CCECKCNLTE KCFSREGKLY CKNDFFRCFG 

        70         80         90        100        110        120 
TKCAGCAQGI SPSDLVRRAR SKVFHLNCFT CMMCNKQLST GEELYIIDEN KFVCKEDYLS 

       130        140        150        160        170        180 
NSSVAKENSL HSATTGSDPS LSPDSQDPSQ DDAKDSESAN VSDKEGGSNE NDDQNLGAKR 

       190        200        210        220        230        240 
RGPRTTIKAK QLETLKAAFA ATPKPTRHIR EQLAQETGLN MRVIQVWFQN RRSKERRMKQ 

       250        260        270        280        290        300 
LSALGARRHA FFRSPRRMRP LVDRLEPGEL IPNGPFSFYG DYQSEYYGPG GNYDFFPQGP 

       310        320        330        340        350        360 
PSSQAQTPVD LPFVPSSGPS GTPLGGLDHP LPGHHPSSEA QRFTDILAHP PGDSPSPEPS 

       370        380        390        400 
LPGPLHSMSA EVFGPSPPFS SLSVNGGASY GNHLSHPPEM NEAAVW 

« Hide

References

[1]"Expression patterns of the murine LIM class homeobox gene lim1 in the developing brain and excretory system."
Fujii T., Pichel J.G., Taira M., Toyama R., Dawid I.B., Westphal H.
Dev. Dyn. 199:73-83(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
Strain: BALB/c.
Tissue: Brain.
[2]"Embryonic expression of Lim-1, the mouse homolog of Xenopus Xlim-1, suggests a role in lateral mesoderm differentiation and neurogenesis."
Barnes J.D., Crosby J.L., Jones C.M., Wright C.V., Hogan B.L.
Dev. Biol. 161:168-178(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
Tissue: Embryo.
[3]"Sequence and genomic organization of the mouse Lim1 gene."
Li Y., Cheah S.S., Deng J.M., Shawlot W., Behringer R.R.
Mamm. Genome 10:444-446(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 129/SvEv.
[4]"The LIM homeodomain protein Lim-1 is widely expressed in neural, neural crest and mesoderm derivatives in vertebrate development."
Karavanov A.A., Saint-Jeannet J.P., Karavanova I., Taira M., Dawid I.B.
Int. J. Dev. Biol. 40:453-461(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[5]"Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins."
Agulnick A.D., Taira M., Breen J.J., Tanaka T., Dawid I.B., Westphal H.
Nature 384:270-272(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LDB1, MUTAGENESIS OF CYS-28 AND CYS-88.
[6]"Interactions between LIM domains and the LIM domain-binding protein Ldb1."
Breen J.J., Agulnick A.D., Westphal H., Dawid I.B.
J. Biol. Chem. 273:4712-4717(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LDB1.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z27410 mRNA. Translation: CAA81797.1.
S68107 mRNA. Translation: AAC60669.2.
AF039706, AF039705 Genomic DNA. Translation: AAD02169.1.
CCDSCCDS25187.1.
PIRI48637.
RefSeqNP_032524.1. NM_008498.2.
UniGeneMm.4965.

3D structure databases

ProteinModelPortalP63006.
SMRP63006. Positions 4-118, 186-236.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid201154. 2 interactions.

Proteomic databases

PRIDEP63006.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000018842; ENSMUSP00000018842; ENSMUSG00000018698.
GeneID16869.
KEGGmmu:16869.
UCSCuc007kqo.1. mouse.

Organism-specific databases

CTD3975.
MGIMGI:99783. Lhx1.

Phylogenomic databases

eggNOGNOG257130.
HOGENOMHOG000231630.
HOVERGENHBG006263.
InParanoidP63006.
KOK09372.
OMADIMSHHP.
OrthoDBEOG7PP56T.
PhylomeDBP63006.
TreeFamTF315442.

Gene expression databases

BgeeP63006.
CleanExMM_LHX1.
GenevestigatorP63006.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
PROSITEPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

NextBio290830.
PROP63006.
SOURCESearch...

Entry information

Entry nameLHX1_MOUSE
AccessionPrimary (citable) accession number: P63006
Secondary accession number(s): P36199
Entry history
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 31, 2004
Last modified: July 9, 2014
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot