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UniProtKB - P63007 (LHX1_RAT)

Entry version 119 (16 Jan 2019)
Sequence version 1 (31 Aug 2004)
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Protein

LIM/homeobox protein Lhx1

Gene

Lhx1

Organism
Rattus norvegicus (Rat)
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

Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis (By similarity).By similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ 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 bindingi180 – 239HomeoboxPROSITE-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

View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

<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 functionDevelopmental protein, DNA-binding
Biological processDifferentiation, 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:
Rlim
<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>OrganismiRattus norvegicus (Rat)
<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 identifieri10116 [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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Rattus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002494 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 10

Organism-specific databases

Rat genome database

More...RGDi		71074 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 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_00000757731 – 406LIM/homeobox protein Lhx1Add BLAST406

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei162PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P63007

PRoteomics IDEntifications database

More...PRIDEi		P63007

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		P63007

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...PhosphoSitePlusi		P63007

<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

Expressed in epithelial structures of the embryonic metanephric kidneys including the ureteric bud and its derivatives, and coma-shaped and S-shaped bodies differentiating from the metanephric mesenchyme. In the adult brain, expressed in the adrenal medulla, Purkinje cells of the cerebellum, hypothalamus, midbrain and pons. Also expressed in the adult testis.2 Publications

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		ENSRNOG00000002812 Expressed in 4 organ(s), highest expression level in adult mammalian kidney

Genevisible search portal to normalized and curated expression data from Genevestigator

More...Genevisiblei		P63007 RN

<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.By similarity

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		10116.ENSRNOP00000003799

<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

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...ProteinModelPortali		P63007

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

More...SMRi		P63007

Database of comparative protein structure models

More...ModBasei		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		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 (By similarity).By similarity

Keywords - Domaini

Homeobox, LIM domain, Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG0490 Eukaryota
ENOG410YIJ3 LUCA

Ensembl GeneTree

More...GeneTreei		ENSGT00940000160834

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000231630

The HOVERGEN Database of Homologous Vertebrate Genes

More...HOVERGENi		HBG006263

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P63007

KEGG Orthology (KO)

More...KOi		K09372

Identification of Orthologs from Complete Genome Data

More...OMAi		DDQNLGG

Database of Orthologous Groups

More...OrthoDBi		1070389at2759

Database for complete collections of gene phylogenies

More...PhylomeDBi		P63007

TreeFam database of animal gene trees

More...TreeFami		TF315442

Family and domain databases

Conserved Domains Database

More...CDDi		cd00086 homeodomain, 1 hit

Integrated resource of protein families, domains and functional sites

More...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

More...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>.<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.

P63007-1 [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
<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:iCC8637984998ADAF
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
S71523 mRNA Translation: AAC60696.1

NCBI Reference Sequences

More...RefSeqi		NP_665887.3, NM_145880.3

UniGene gene-oriented nucleotide sequence clusters

More...UniGenei		Rn.127825

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSRNOT00000003799; ENSRNOP00000003799; ENSRNOG00000002812

Database of genes from NCBI RefSeq genomes

More...GeneIDi		257634

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		rno:257634

<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
S71523 mRNA Translation: AAC60696.1
RefSeqiNP_665887.3, NM_145880.3
UniGeneiRn.127825

3D structure databases

ProteinModelPortaliP63007
SMRiP63007
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000003799

PTM databases

iPTMnetiP63007
PhosphoSitePlusiP63007

Proteomic databases

PaxDbiP63007
PRIDEiP63007

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000003799; ENSRNOP00000003799; ENSRNOG00000002812
GeneIDi257634
KEGGirno:257634

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		3975
RGDi71074 Lhx1

Phylogenomic databases

eggNOGiKOG0490 Eukaryota
ENOG410YIJ3 LUCA
GeneTreeiENSGT00940000160834
HOGENOMiHOG000231630
HOVERGENiHBG006263
InParanoidiP63007
KOiK09372
OMAiDDQNLGG
OrthoDBi1070389at2759
PhylomeDBiP63007
TreeFamiTF315442

Miscellaneous databases

Protein Ontology

More...PROi		PR:P63007

Gene expression databases

BgeeiENSRNOG00000002812 Expressed in 4 organ(s), highest expression level in adult mammalian kidney
GenevisibleiP63007 RN

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...

<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_RAT
<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: P63007
Secondary accession number(s): P36199
<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: August 31, 2004
Last sequence update: August 31, 2004
Last modified: January 16, 2019
This is version 119 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

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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