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Entry version 124 (18 Sep 2019)
Sequence version 1 (01 Apr 1993)
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Protein

LIM/homeobox protein Lhx1

Gene

lhx1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Involved in the establishment of the body plan via the Spemann organizer during gastrulation. Transcriptional activator required to induce organizer gene expression downstream of siamois. Promotes head formation by binding to 5'-TAAT'-3' elements in the promoters of head organizer genes cer1 and gsc to stimulate expression. Binds as a complex with siamois and mix-A/mix.1 to the cer1 promoter, and with ldb1 and otx2 to the gsc promoter. Also involved in neural induction via the organizer, including a role in notochord formation. Acts synergistically with ldb1 and ssbp in subsequent axis formation. Involved in kidney development, acting synergistically with pax8 to establish the pronephric primordium in late gastrulae/early neurulae and with pax2 during pronephric morphogenesis in tailbud stages. Has a later role in mediating the activity of inhibitors of ventralization.13 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi179 – 238HomeoboxPROSITE-ProRule annotationAdd BLAST60

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionActivator, Developmental protein, DNA-binding
Biological processDifferentiation, Gastrulation, Neurogenesis, Transcription, Transcription regulation
LigandMetal-binding, Zinc

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
LIM/homeobox protein Lhx1
Short name:
LIM homeobox protein 1
Alternative name(s):
Homeobox protein Lim-1
Short name:
Xlim1
Short name:
x-Lhx1
Short name:
xLIM-1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:lhx1
Synonyms:lim-1, lim1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiXenopus laevis (African clawed frog)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri8355 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

Xenopus laevis and tropicalis biology and genomics resource

More...
Xenbasei
XB-GENE-856460 lhx1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi28C → G: Disrupts ldb1-binding. Produces an active form; when associated with G-88. 2 Publications1
Mutagenesisi88C → G: Disrupts ldb1-binding. Produces an active form; when associated with G-28. 2 Publications1
Mutagenesisi223I → P: Fails to induce chrd. 1 Publication1
Mutagenesisi278Y → A: Abolishes transcriptional activity and axis-inducing activity; when associated with A-281; A-285; A-286 and A-292. 1 Publication1
Mutagenesisi278Y → F: No effect on axis-inducing activity; when associated with F-281; F-285; F-286 and F-292. 1 Publication1
Mutagenesisi281Y → A: Abolishes transcriptional activity and axis-inducing activity; when associated with A-278; A-285; A-286 and A-292. 1 Publication1
Mutagenesisi281Y → F: No effect on axis-inducing activity; when associated with F-278; F-285; F-286 and F-292. 1 Publication1
Mutagenesisi285Y → A: Abolishes transcriptional activity and axis-inducing activity; when associated with A-278; A-281; A-286 and A-292. 1 Publication1
Mutagenesisi285Y → F: No effect on axis-inducing activity; when associated with F-278; F-281; F-286 and F-292. 1 Publication1
Mutagenesisi286Y → A: Abolishes transcriptional activity and axis-inducing activity; when associated with A-278; A-281; A-285 and A-292. 1 Publication1
Mutagenesisi286Y → F: No effect on axis-inducing activity; when associated with F-278; F-281; F-285 and F-292. 1 Publication1
Mutagenesisi292Y → A: Abolishes transcriptional activity and axis-inducing activity; when associated with A-278; A-281; A-285 and A-286. 1 Publication1
Mutagenesisi292Y → F: No effect on axis-inducing activity; when associated with F-278; F-281; F-285 and F-286. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000757771 – 403LIM/homeobox protein Lhx1Add BLAST403

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Exhibits a biphasic expression pattern. Initially localized to the Spemann organizer region of gastrulae, leading to expression in prechordal mesoderm and notochord. In the second phase, expressed in the lateral mesoderm and neural plate, eventually concentrating in the pronephros and the CNS. Expressed in the pronephros primordium by late gastrula (stage 12.5) and becomes restricted to the tips of the tubules and ducts as kidney development progresses. In the CNS, becomes progressively recognizable in anatomically distinct structures during larval development. Within the forebrain, shows almost identical expression to lhx5 in the diencephalon, being expressed in alternating stripes to lhx2 and lhx9. Expressed in the diencephalic pretectum within prosomere 1, hypothalamus, ventral thalamus and zona limitans intrathalamica. In the telencephalon, the expression pattern is distinct from lhx5, being localized in the pallium and subpallium. Also expressed in the ventral territories of midbrain (mesencephalon) and hindbrain (rhombencephalon), being expressed in the mesencephalic tegmentum and hindbrain reticular formation. Also shows intense expression in the cerebellum including Purkinje cells.10 Publications

<p>This subsection of the ‘Expression’ section provides information on the expression of the gene product at various stages of a cell, tissue or organism development. By default, the information is derived from experiments at the mRNA level, unless specified ‘at the protein level’.<p><a href='/help/developmental_stage' target='_top'>More...</a></p>Developmental stagei

Expressed both maternally and zygotically. Expressed at a low level in the unfertilized egg. Expression is highest at the gastrula stage, then declines before rising again during the tadpole stage.1 Publication

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

By retinoic acid and by dorsal mesoderm-inducers including activin, derriere, dvr1/vg-1 and nodal.6 Publications

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts with ldb1 via the tandem LIM domains. Both LIM domains are required for optimal binding and binding relieves the inhibitory effect of the LIM domains and activates lhx1. Binding to ldb1 also prevents degradation of ldb1 by rnf12. The stoichiometry of lhx1 and ldb1 is important for their function and an excess of ldb1 can inhibit lhx1 function.

Interacts with the N-terminal region of rnf12 by a homeobox-dependent mechanism.

3 Publications

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P29674

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini4 – 54LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST51
Domaini63 – 117LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST55

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>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.2 Publications

Keywords - Domaini

Homeobox, LIM domain, Repeat

Phylogenomic databases

KEGG Orthology (KO)

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KOi
K09372

Database of Orthologous Groups

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OrthoDBi
1070389at2759

Family and domain databases

Conserved Domains Database

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CDDi
cd00086 homeodomain, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR001781 Znf_LIM

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00046 Homeodomain, 1 hit
PF00412 LIM, 2 hits

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00389 HOX, 1 hit
SM00132 LIM, 2 hits

Superfamily database of structural and functional annotation

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SUPFAMi
SSF46689 SSF46689, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit
PS00478 LIM_DOMAIN_1, 2 hits
PS50023 LIM_DOMAIN_2, 2 hits

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P29674-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVHCAGCERP ILDRFLLNVL DRAWHVKCVQ CCECKCNLTE KCFSREGKLY
60 70 80 90 100
CKNDFFRRFG TKCAGCAQGI SPSDLVRRAR SKVFHLNCFT CMMCNKQLST
110 120 130 140 150
GEELYIIDEN KFVCKEDYLN NNNAAKENSF ISVTGSDPSL SPESQDPLQD
160 170 180 190 200
DAKDSESANV SDKEAGINEN DDQNLGAKRR GPRTTIKAKQ LETLKAAFAA
210 220 230 240 250
TPKPTRHIRE QLAQETGLNM RVIQVWFQNR RSKERRMKQL SALGARRHAF
260 270 280 290 300
FRSPRRMRPL VDRLEPGELI PNGPFAFYGD YQSEYYGPGS NYDFFPQGPP
310 320 330 340 350
SSQAQTPVDL PFVPSSVPAG TPLGAMDHPI PGHHPSSDAQ RFTDIMSHPP
360 370 380 390 400
GDSPSPEPNL PGSMHSMSAE VFGQSPPFSS LSVNGGYGNH LSHPPEMNET

AVW
Length:403
Mass (Da):44,935
Last modified:April 1, 1993 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i4147EB3A2774C110
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
X63889 mRNA Translation: CAA45353.1
AF013242 Genomic DNA Translation: AAB70190.1

Protein sequence database of the Protein Information Resource

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PIRi
S23802

NCBI Reference Sequences

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RefSeqi
NP_001084128.1, NM_001090659.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

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GeneIDi
399323

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
xla:399323

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X63889 mRNA Translation: CAA45353.1
AF013242 Genomic DNA Translation: AAB70190.1
PIRiS23802
RefSeqiNP_001084128.1, NM_001090659.1

3D structure databases

SMRiP29674
ModBaseiSearch...

Genome annotation databases

GeneIDi399323
KEGGixla:399323

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
399323
XenbaseiXB-GENE-856460 lhx1

Phylogenomic databases

KOiK09372
OrthoDBi1070389at2759

Family and domain databases

CDDicd00086 homeodomain, 1 hit
InterProiView protein in InterPro
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR001781 Znf_LIM
PfamiView protein in Pfam
PF00046 Homeodomain, 1 hit
PF00412 LIM, 2 hits
SMARTiView protein in SMART
SM00389 HOX, 1 hit
SM00132 LIM, 2 hits
SUPFAMiSSF46689 SSF46689, 1 hit
PROSITEiView protein in PROSITE
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit
PS00478 LIM_DOMAIN_1, 2 hits
PS50023 LIM_DOMAIN_2, 2 hits

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiLHX1_XENLA
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P29674
Secondary accession number(s): Q9PSU2
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: September 18, 2019
This is version 124 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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