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Protein

LIM/homeobox protein Lhx1

Gene

Lhx1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi180 – 23960HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • anatomical structure formation involved in morphogenesis Source: MGI
  • anatomical structure morphogenesis Source: MGI
  • anterior/posterior axis specification Source: MGI
  • anterior/posterior pattern specification Source: MGI
  • branching involved in ureteric bud morphogenesis Source: UniProtKB
  • cell-cell signaling Source: MGI
  • cellular response to fibroblast growth factor stimulus Source: Ensembl
  • cerebellar Purkinje cell differentiation Source: MGI
  • cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation Source: MGI
  • cerebellum development Source: MGI
  • cervix development Source: UniProtKB
  • comma-shaped body morphogenesis Source: UniProtKB
  • dorsal/ventral pattern formation Source: MGI
  • ectoderm formation Source: MGI
  • embryonic pattern specification Source: MGI
  • embryonic retina morphogenesis in camera-type eye Source: UniProtKB
  • embryonic viscerocranium morphogenesis Source: UniProtKB
  • endoderm formation Source: MGI
  • epithelium development Source: UniProtKB
  • forebrain regionalization Source: MGI
  • gastrulation with mouth forming second Source: MGI
  • head development Source: UniProtKB
  • horizontal cell localization Source: UniProtKB
  • kidney development Source: MGI
  • lateral motor column neuron migration Source: UniProtKB
  • mesonephric duct development Source: Ensembl
  • mesonephros development Source: UniProtKB
  • metanephric comma-shaped body morphogenesis Source: Ensembl
  • metanephric glomerulus development Source: Ensembl
  • metanephric part of ureteric bud development Source: Ensembl
  • metanephric renal vesicle morphogenesis Source: UniProtKB
  • metanephric S-shaped body morphogenesis Source: UniProtKB
  • metanephros development Source: UniProtKB
  • motor neuron axon guidance Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • nephric duct elongation Source: UniProtKB
  • nephric duct morphogenesis Source: UniProtKB
  • oviduct development Source: UniProtKB
  • oviduct epithelium development Source: UniProtKB
  • paramesonephric duct development Source: UniProtKB
  • pattern specification process Source: MGI
  • positive regulation of anterior head development Source: UniProtKB
  • positive regulation of branching involved in ureteric bud morphogenesis Source: UniProtKB
  • positive regulation of embryonic development Source: UniProtKB
  • positive regulation of gastrulation Source: UniProtKB
  • positive regulation of nephron tubule epithelial cell differentiation Source: UniProtKB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • post-embryonic development Source: MGI
  • primitive streak formation Source: UniProtKB
  • pronephros development Source: UniProtKB
  • regulation of gene expression Source: MGI
  • renal system development Source: MGI
  • renal vesicle morphogenesis Source: UniProtKB
  • retina development in camera-type eye Source: UniProtKB
  • retina layer formation Source: UniProtKB
  • somite rostral/caudal axis specification Source: MGI
  • spinal cord association neuron differentiation Source: UniProtKB
  • spinal cord development Source: UniProtKB
  • S-shaped body morphogenesis Source: UniProtKB
  • telencephalon development Source: UniProtKB
  • transcription from RNA polymerase II promoter Source: UniProtKB
  • ureteric bud development Source: MGI
  • urogenital system development Source: MGI
  • uterine epithelium development Source: UniProtKB
  • uterus development Source: UniProtKB
  • vagina development Source: UniProtKB
  • ventral spinal cord development Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
LIM/homeobox protein Lhx1
Short name:
LIM homeobox protein 1
Alternative name(s):
Homeobox protein Lim-1
Gene namesi
Name:Lhx1
Synonyms:Lim-1, Lim1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:99783. Lhx1.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation1 Publication

GO - Cellular componenti

  • intracellular Source: MGI
  • nucleus Source: UniProtKB
  • protein complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi28 – 281C → G: Disrupts LDB1-binding; when associated with G-88. 1 Publication
Mutagenesisi88 – 881C → G: Disrupts LDB1-binding; when associated with G-28. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 406406LIM/homeobox protein Lhx1PRO_0000075771Add
BLAST

Proteomic databases

MaxQBiP63006.
PRIDEiP63006.

Expressioni

Tissue specificityi

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.3 Publications

Developmental stagei

Expressed in both embryos and adults.1 Publication

Gene expression databases

BgeeiP63006.
CleanExiMM_LHX1.
ExpressionAtlasiP63006. baseline and differential.
GenevisibleiP63006. MM.

Interactioni

Subunit structurei

Interacts with LDB1 via the tandem LIM domains.2 Publications

Protein-protein interaction databases

BioGridi201154. 2 interactions.
STRINGi10090.ENSMUSP00000018842.

Structurei

3D structure databases

ProteinModelPortaliP63006.
SMRiP63006. Positions 4-118, 186-236.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 5451LIM zinc-binding 1PROSITE-ProRule annotationAdd
BLAST
Domaini63 – 11755LIM zinc-binding 2PROSITE-ProRule annotationAdd
BLAST

Domaini

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).By similarity

Sequence similaritiesi

Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation
Contains 2 LIM zinc-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox, LIM domain, Repeat

Phylogenomic databases

eggNOGiNOG257130.
HOGENOMiHOG000231630.
HOVERGENiHBG006263.
InParanoidiP63006.
KOiK09372.
OMAiSVTACSD.
OrthoDBiEOG7PP56T.
PhylomeDBiP63006.
TreeFamiTF315442.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P63006-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVHCAGCKRP ILDRFLLNVL DRAWHVKCVQ CCECKCNLTE KCFSREGKLY
60 70 80 90 100
CKNDFFRCFG TKCAGCAQGI SPSDLVRRAR SKVFHLNCFT CMMCNKQLST
110 120 130 140 150
GEELYIIDEN KFVCKEDYLS NSSVAKENSL HSATTGSDPS LSPDSQDPSQ
160 170 180 190 200
DDAKDSESAN VSDKEGGSNE NDDQNLGAKR RGPRTTIKAK QLETLKAAFA
210 220 230 240 250
ATPKPTRHIR EQLAQETGLN MRVIQVWFQN RRSKERRMKQ LSALGARRHA
260 270 280 290 300
FFRSPRRMRP LVDRLEPGEL IPNGPFSFYG DYQSEYYGPG GNYDFFPQGP
310 320 330 340 350
PSSQAQTPVD LPFVPSSGPS GTPLGGLDHP LPGHHPSSEA QRFTDILAHP
360 370 380 390 400
PGDSPSPEPS LPGPLHSMSA EVFGPSPPFS SLSVNGGASY GNHLSHPPEM

NEAAVW
Length:406
Mass (Da):44,780
Last modified:August 31, 2004 - v1
Checksum:iCC8637984998ADAF
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti12 – 121L → LARQVRPVL (PubMed:7904966).Curated
Sequence conflicti24 – 318Missing in AAC60669 (PubMed:7904966).Curated
Sequence conflicti236 – 2361R → A in AAC60669 (PubMed:7904966).Curated
Sequence conflicti335 – 3351H → HH in AAC60669 (PubMed:7904966).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z27410 mRNA. Translation: CAA81797.1.
S68107 mRNA. Translation: AAC60669.2.
AF039706, AF039705 Genomic DNA. Translation: AAD02169.1.
CCDSiCCDS25187.1.
PIRiI48637.
RefSeqiNP_032524.1. NM_008498.2.
UniGeneiMm.4965.

Genome annotation databases

EnsembliENSMUST00000018842; ENSMUSP00000018842; ENSMUSG00000018698.
GeneIDi16869.
KEGGimmu:16869.
UCSCiuc007kqo.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z27410 mRNA. Translation: CAA81797.1.
S68107 mRNA. Translation: AAC60669.2.
AF039706, AF039705 Genomic DNA. Translation: AAD02169.1.
CCDSiCCDS25187.1.
PIRiI48637.
RefSeqiNP_032524.1. NM_008498.2.
UniGeneiMm.4965.

3D structure databases

ProteinModelPortaliP63006.
SMRiP63006. Positions 4-118, 186-236.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi201154. 2 interactions.
STRINGi10090.ENSMUSP00000018842.

Proteomic databases

MaxQBiP63006.
PRIDEiP63006.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000018842; ENSMUSP00000018842; ENSMUSG00000018698.
GeneIDi16869.
KEGGimmu:16869.
UCSCiuc007kqo.1. mouse.

Organism-specific databases

CTDi3975.
MGIiMGI:99783. Lhx1.

Phylogenomic databases

eggNOGiNOG257130.
HOGENOMiHOG000231630.
HOVERGENiHBG006263.
InParanoidiP63006.
KOiK09372.
OMAiSVTACSD.
OrthoDBiEOG7PP56T.
PhylomeDBiP63006.
TreeFamiTF315442.

Miscellaneous databases

NextBioi290830.
PROiP63006.
SOURCEiSearch...

Gene expression databases

BgeeiP63006.
CleanExiMM_LHX1.
ExpressionAtlasiP63006. baseline and differential.
GenevisibleiP63006. MM.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  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.

Entry informationi

Entry nameiLHX1_MOUSE
AccessioniPrimary (citable) accession number: P63006
Secondary accession number(s): P36199
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 31, 2004
Last modified: June 24, 2015
This is version 106 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.