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UniProtKB - Q9LW68 (LSH4_ARATH)

Entry version 92 (12 Aug 2020)
Sequence version 1 (01 Oct 2000)
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Protein

Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4

Gene

LSH4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score:

Annotation score:4 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

Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light (By similarity). May suppress organ differentiation in the boundary region.By similarity1 Publication

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

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 processTranscription, Transcription regulation

<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%5Fand%5Ftaxonomy%5Fsection">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:
Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4
Alternative name(s):
Protein ORGAN BOUNDARY 4
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:LSH4
Synonyms:OBO4
Ordered Locus Names:At3g23290
ORF Names:MLM24
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiArabidopsis thaliana (Mouse-ear cress)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri3702 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliopsida › eudicotyledons › Gunneridae › Pentapetalae › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000006548 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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 3

Organism-specific databases

Arabidopsis Information Portal

More...Araporti		AT3G23290

The Arabidopsis Information Resource

More...TAIRi		locus:2082170, AT3G23290

<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 Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics 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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004252911 – 195Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4Add BLAST195

Proteomic databases

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

More...PaxDbi		Q9LW68

PRoteomics IDEntifications database

More...PRIDEi		Q9LW68

ProteomicsDB: a multi-organism proteome resource

More...ProteomicsDBi		238531

<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

Induced by NAC054/CUC1 and NAC098/CUC2 in shoot organ boundary cells.1 Publication

<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

Accumulates at the boundaries between the apical meristems and lateral organs in embryos, seedlings, and mature plants, and at the root apical meristem and in distinct cell files surrounding this area. First observed in the shoot apex of early-heart embryos. Within the apex of the late-heart stage embryo, the signal is detected in the peripheral region but not in the central region. At the bent-cotyledon stage, accumulates in boundary cells located between the shoot apical meristem (SAM) and the cotyledon primordia. In seedlings, weakly expressed in the basal cells of the leaf primordia. During the reproductive phase, present in boundary cells between the SAM and the flower primordia, and in boundary cells between the floral meristem and sepal primordia. In developing flowers, confined to regions that surround the floral organs at the base.1 Publication

Gene expression databases

ExpressionAtlas, Differential and Baseline Expression

More...ExpressionAtlasi		Q9LW68, baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...Genevisiblei		Q9LW68, AT

<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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		7240, 3 interactors

Protein interaction database and analysis system

More...IntActi		Q9LW68, 3 interactors

STRING: functional protein association networks

More...STRINGi		3702.AT3G23290.2

<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%5Fand%5Fdomains%5Fsection">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>Domaini48 – 175ALOGPROSITE-ProRule annotationAdd BLAST128

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi173 – 177Nuclear localization signalBy similarity5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi31 – 38Poly-Ser8
Compositional biasi179 – 185Poly-Pro7

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the plant homeotic and developmental regulators ALOG protein family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG502QT0B, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_071168_1_0_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q9LW68

Identification of Orthologs from Complete Genome Data

More...OMAi		NNSMTML

Database of Orthologous Groups

More...OrthoDBi		1337441at2759

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q9LW68

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR040222, ALOG
IPR006936, ALOG_dom

The PANTHER Classification System

More...PANTHERi		PTHR31165, PTHR31165, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF04852, DUF640, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51697, ALOG, 1 hit

<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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

Q9LW68-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDHIIGFMGT TNMSHNTNLM IAAAATTTTT SSSSSSSSGG SGTNQLSRYE 
        60         70         80         90        100
NQKRRDWNTF GQYLRNHRPP LSLSRCSGAH VLEFLRYLDQ FGKTKVHTHL 
       110        120        130        140        150
CPFFGHPNPP APCACPLRQA WGSLDALIGR LRAAFEENGG SPETNPFGAR 
       160        170        180        190 
AVRLYLREVR DSQAKARGIS YEKKKRKRPP PPLPPAQPAI SSSPN
Length:195
Mass (Da):21,434
Last modified:October 1, 2000 - 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:iA6BA85958BEFCE23
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAR24161 differs from that shown. Reason: Erroneous initiation. Truncated N-terminus.Curated

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
AB015474, AP000733 Genomic DNA Translation: BAB02272.1
CP002686 Genomic DNA Translation: AEE76748.1
BT010794 mRNA Translation: AAR24161.1 Different initiation.
BT011275 mRNA Translation: AAR92311.1

NCBI Reference Sequences

More...RefSeqi		NP_001078202.2, NM_001084733.2

Genome annotation databases

Ensembl plant genome annotation project

More...EnsemblPlantsi		AT3G23290.2; AT3G23290.2; AT3G23290

Database of genes from NCBI RefSeq genomes

More...GeneIDi		821908

Gramene; a comparative resource for plants

More...Gramenei		AT3G23290.2; AT3G23290.2; AT3G23290

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ath:AT3G23290

<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
AB015474, AP000733 Genomic DNA Translation: BAB02272.1
CP002686 Genomic DNA Translation: AEE76748.1
BT010794 mRNA Translation: AAR24161.1 Different initiation.
BT011275 mRNA Translation: AAR92311.1
RefSeqiNP_001078202.2, NM_001084733.2

3D structure databases

Database of comparative protein structure models

More...ModBasei		Search...

SWISS-MODEL Interactive Workspace

More...SWISS-MODEL-Workspacei		Submit a new modelling project...

Protein-protein interaction databases

BioGRIDi7240, 3 interactors
IntActiQ9LW68, 3 interactors
STRINGi3702.AT3G23290.2

Proteomic databases

PaxDbiQ9LW68
PRIDEiQ9LW68
ProteomicsDBi238531

Genome annotation databases

EnsemblPlantsiAT3G23290.2; AT3G23290.2; AT3G23290
GeneIDi821908
GrameneiAT3G23290.2; AT3G23290.2; AT3G23290
KEGGiath:AT3G23290

Organism-specific databases

AraportiAT3G23290
TAIRilocus:2082170, AT3G23290

Phylogenomic databases

eggNOGiENOG502QT0B, Eukaryota
HOGENOMiCLU_071168_1_0_1
InParanoidiQ9LW68
OMAiNNSMTML
OrthoDBi1337441at2759
PhylomeDBiQ9LW68

Miscellaneous databases

Protein Ontology

More...PROi		PR:Q9LW68

Gene expression databases

ExpressionAtlasiQ9LW68, baseline and differential
GenevisibleiQ9LW68, AT

Family and domain databases

InterProiView protein in InterPro
IPR040222, ALOG
IPR006936, ALOG_dom
PANTHERiPTHR31165, PTHR31165, 1 hit
PfamiView protein in Pfam
PF04852, DUF640, 1 hit
PROSITEiView protein in PROSITE
PS51697, ALOG, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...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 nameiLSH4_ARATH
<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: Q9LW68
Secondary accession number(s): Q6NNL1
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 19, 2014
Last sequence update: October 1, 2000
Last modified: August 12, 2020
This is version 92 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 programPlant 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

Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families
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