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UniProtKB - B3DJE0 (B3DJE0_DANRE)

Entry version 81 (13 Feb 2019)
Sequence version 1 (22 Jul 2008)
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Protein
Submitted name:

SRY (sex determining region Y)-box 5

Gene

sox5

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Unreviewed-Annotation score:

Annotation score:2 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

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 bindingi558 – 626HMG boxPROSITE-ProRule annotationAdd BLAST69

<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 functionDNA-bindingPROSITE-ProRule annotationSAAS annotation

<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
Submitted name:
SRY (sex determining region Y)-box 5Imported
Submitted name:
SRY-box containing gene 5Imported
<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:sox5Imported
<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>OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)Imported
<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 identifieri7955 [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 › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Cyprinidae › Danio
<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
  • UP000000437 <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 4

Organism-specific databases

Zebrafish Information Network genome database

More...ZFINi		ZDB-GENE-000607-13 sox5

<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; Source: COMPARTMENTS

Keywords - Cellular componenti

NucleusPROSITE-ProRule annotation

<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

Proteomic databases

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

More...PaxDbi		B3DJE0

PeptideAtlas

More...PeptideAtlasi		B3DJE0

<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

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		ENSDARG00000011582 Expressed in 38 organ(s), highest expression level in presomitic mesoderm

ExpressionAtlas, Differential and Baseline Expression

More...ExpressionAtlasi		B3DJE0 baseline

<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

STRING: functional protein association networks

More...STRINGi		7955.ENSDARP00000023698

<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>Domaini558 – 626HMG boxInterPro annotationAdd BLAST69

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and domains’ section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili189 – 209Sequence analysisAdd BLAST21
Coiled coili211 – 269Sequence analysisAdd BLAST59
Coiled coili457 – 487Sequence analysisAdd BLAST31
Coiled coili498 – 518Sequence analysisAdd BLAST21

Keywords - Domaini

Coiled coilSequence analysis

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG0528 Eukaryota
ENOG410YZNG LUCA

Ensembl GeneTree

More...GeneTreei		ENSGT00940000156122

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000056455

The HOVERGEN Database of Homologous Vertebrate Genes

More...HOVERGENi		HBG003915

Identification of Orthologs from Complete Genome Data

More...OMAi		MRQYFSV

TreeFam database of animal gene trees

More...TreeFami		TF320471

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.30.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR009071 HMG_box_dom
IPR036910 HMG_box_dom_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00505 HMG_box, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00398 HMG, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF47095 SSF47095, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50118 HMG_BOX_2, 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_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>Sequence (1+)i

<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.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

B3DJE0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLTEPELPQE FNRMSSKRPA SPYGGTDGEV VMATSRQRLE DEEVDGHAVI 
        60         70         80         90        100
HLPLSSYCSK VSPRSPRLLD SPPTLHANMD QDGSKGLALS PYAQHNSSTS 
       110        120        130        140        150
PSKQQQEDSS MRPGSEPGSA SALGTPERRK GSLADVVDTL KQRKMEELIK 
       160        170        180        190        200
NEPEEAPSIE RLLSKDWKDK LLAMGSGNFG EIKGTPDSLA EKERQLMGMI 
       210        220        230        240        250
TQLSSLREQL LAAHEEQKKL AASQIEKQRQ QMELAKQQQD QIARQQQQLL 
       260        270        280        290        300
QQQHKINLLQ QQIQQVQGQL PPLMIPVFPP DQRTLAAAAA QQGFLLPPGF 
       310        320        330        340        350
NYKPGCSEPY PLQLIPTTMA AAAAATPGLG PLQLQQLYAA QLAAMQVSPG 
       360        370        380        390        400
AKHSTVPQAN LATGTLSPTS GQSEKNRSTP PPKPKDEGAQ PLNLSSKPKA 
       410        420        430        440        450
SESKSPTSPA SPQVPALKLG PGSLKHSAPS SIGGPPSRLS SIDLLSSITS 
       460        470        480        490        500
AGYLNDHEAV TKAFQEARKM KEQLKREEQV LDAKVAAVNS LSLNNGRSEK 
       510        520        530        540        550
EKAALESLSQ QLKQSEESKF THAMMDFGIS GDSDGSPSVS DSRIFREARG 
       560        570        580        590        600
RGSSEPHIKR PMNAFMVWAK DERRKILQAF PDMHNSNISK ILGSRWKSMT 
       610        620        630        640        650
NLEKQPYYEE QARLSKQHLE KYPDYKYKPR PKRTCLVDGK KLRIGEYKAI 
       660        670        680        690        700
MRNRRQEMRQ YFTVGQQAQL PLSSAGVVYP GALSMAGMPS PQMPSEHSSM 
       710        720        730        740        750
SSSPEPVPPT SQASYFKEVE PRVKEELRMD DGNGDAYDDF DYEDDDGDYG 

SDSENHITQ
Length:759
Mass (Da):83,508
Last modified:July 22, 2008 - 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:iF2EC7B4432B8C534
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q5RH23Q5RH23_DANRE
SRY (sex determining region Y)-box ...
sox5
757Annotation score:

Annotation score:2 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>

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
BX649261 Genomic DNA No translation available.
CR792413 Genomic DNA No translation available.
BC163449 mRNA Translation: AAI63449.1

UniGene gene-oriented nucleotide sequence clusters

More...UniGenei		Dr.101350

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSDART00000162945; ENSDARP00000137633; ENSDARG00000011582

<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
BX649261 Genomic DNA No translation available.
CR792413 Genomic DNA No translation available.
BC163449 mRNA Translation: AAI63449.1
UniGeneiDr.101350

3D structure databases

Database of comparative protein structure models

More...ModBasei		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000023698

Proteomic databases

PaxDbiB3DJE0
PeptideAtlasiB3DJE0

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000162945; ENSDARP00000137633; ENSDARG00000011582

Organism-specific databases

ZFINiZDB-GENE-000607-13 sox5

Phylogenomic databases

eggNOGiKOG0528 Eukaryota
ENOG410YZNG LUCA
GeneTreeiENSGT00940000156122
HOGENOMiHOG000056455
HOVERGENiHBG003915
OMAiMRQYFSV
TreeFamiTF320471

Gene expression databases

BgeeiENSDARG00000011582 Expressed in 38 organ(s), highest expression level in presomitic mesoderm
ExpressionAtlasiB3DJE0 baseline

Family and domain databases

Gene3Di1.10.30.10, 1 hit
InterProiView protein in InterPro
IPR009071 HMG_box_dom
IPR036910 HMG_box_dom_sf
PfamiView protein in Pfam
PF00505 HMG_box, 1 hit
SMARTiView protein in SMART
SM00398 HMG, 1 hit
SUPFAMiSSF47095 SSF47095, 1 hit
PROSITEiView protein in PROSITE
PS50118 HMG_BOX_2, 1 hit

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 nameiB3DJE0_DANRE
<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: B3DJE0
Secondary accession number(s): A0A0R4INR5
<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/TrEMBL: July 22, 2008
Last sequence update: July 22, 2008
Last modified: February 13, 2019
This is version 81 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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, Proteomics identificationCombined sources, Reference proteomeImported
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