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UniProtKB - X1WGX5 (PUM3_DANRE)

Entry version 38 (08 May 2019)
Sequence version 2 (20 Jan 2016)
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Protein

Pumilio homolog 3

Gene

pum3

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
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 transcript 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

Inhibits the poly(ADP-ribosyl)ation activity of PARP1 and the degradation of PARP1 by CASP3 following genotoxic stress (By similarity). Binds to double-stranded RNA or DNA without sequence specificity (By similarity). Involved in development of the eye and of primordial germ cells (PubMed:19319195).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

View the complete GO annotation on QuickGO ...

GO - Biological processi

  • germ cell migration Source: ZFIN
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-binding, RNA-binding

<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:
Pumilio homolog 3Curated
<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:pum3
Synonyms:puf-a1 Publication
<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 10

Organism-specific databases

Zebrafish Information Network genome database

More...ZFINi		ZDB-GENE-030131-9808 pum3

<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

Chromosome, 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

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Morpholino knockdown in embryos results in small eyes, small head and brain edema at 1 and 2 days post-fertilization (dpf). At 3 and 5 dpf, mutants exhibit features of an undifferentiated retina with loss of detailed architecture and a significant reduction in eye size. Structures such as the rod and cone layers are not concentrically organized and retinal ganglion cells and plexiform layers are not readily discernible. Mutants also show abnormal primordial germ cell migration.1 Publication

<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_00004353331 – 629Pumilio homolog 3Add BLAST629

Proteomic databases

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

More...PaxDbi		X1WGX5

<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

In adult, expressed at high levels in eye and ovary and at lower levels in brain, testis and head kidney. In the adult ovary, prominently expressed in early immature follicles.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

Expressed throughout embryogenesis. In the adult ovary, strong expression detected in primitive stage I ovarian follicles with levels declining sharply and becoming negligible in subsequent stages of oocyte development.1 Publication

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		ENSDARG00000087779 Expressed in 32 organ(s), highest expression level in presomitic mesoderm

ExpressionAtlas, Differential and Baseline Expression

More...ExpressionAtlasi		X1WGX5 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.ENSDARP00000129484

<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

More...SMRi		X1WGX5

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>Domaini120 – 473PUM-HDPROSITE-ProRule annotationAdd BLAST354
<p>This subsection of the ‘Family and Domains’ section indicates the positions and types of repeated sequence motifs or repeated domains within the protein.<p><a href='/help/repeat' target='_top'>More...</a></p>Repeati160 – 195Pumilio 1By similarityAdd BLAST36
Repeati196 – 231Pumilio 2By similarityAdd BLAST36
Repeati232 – 260Pumilio 3By similarityAdd BLAST29
Repeati272 – 308Pumilio 4By similarityAdd BLAST37
Repeati309 – 344Pumilio 5By similarityAdd BLAST36
Repeati345 – 380Pumilio 6By similarityAdd BLAST36
Repeati381 – 418Pumilio 7By similarityAdd BLAST38
Repeati419 – 487Pumilio 8By similarityAdd BLAST69
Repeati488 – 534Pumilio 9By similarityAdd BLAST47
Repeati535 – 579Pumilio 10By similarityAdd BLAST45
Repeati580 – 618Pumilio 11By similarityAdd BLAST39

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>Motifi88 – 100Nuclear localization signalBy similarityAdd BLAST13

<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

A 90 degree bend between Pumilio repeats 3 and 4 gives rise to a L-shaped protein.By similarity

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG2050 Eukaryota
ENOG410XSHY LUCA

Ensembl GeneTree

More...GeneTreei		ENSGT00390000015757

Identification of Orthologs from Complete Genome Data

More...OMAi		YLQEHAQ

Database of Orthologous Groups

More...OrthoDBi		845051at2759

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.25.10.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR011989 ARM-like
IPR016024 ARM-type_fold
IPR012959 CPL_dom
IPR033133 PUM-HD
IPR040059 PUM3
IPR001313 Pumilio_RNA-bd_rpt

The PANTHER Classification System

More...PANTHERi		PTHR13389 PTHR13389, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF08144 CPL, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00025 Pumilio, 6 hits

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF48371 SSF48371, 2 hits

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50302 PUM, 5 hits
PS50303 PUM_HD, 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 2 potential isoforms that are computationally mapped.Show allAlign All

X1WGX5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEGKPRKKSF TPRDGKKPSF KSKGKPGGKP QGKRPFKPHN NDKGKGFRKS 
        60         70         80         90        100
GGEGGPQKFN RKPTDGKFAK KRKFPGDRIK QEEGDERKKP KWDEFKQKKK 
       110        120        130        140        150
ELKLNRQQTD RKESYQIVSR AKQVWEMVRR KDCDKQKRTK LMKELQDLVK 
       160        170        180        190        200
GKIKTIAFAH DSTRVLQCFI QFGSDKQRKE VFDELKEHIV ELSKSKYARN 
       210        220        230        240        250
IVKKFLMYGS KEQVGEVMLA FKGKVRQMLR HSEASSVVEY AYNDKAILSQ 
       260        270        280        290        300
RLMLTEELYG NTFTVLKSSV CPTLEKVLEA NPGKLESILD EMKQILTPMA 
       310        320        330        340        350
QKEAVIKHSL VHKVFLDFFE HAPDKQRTEM IESIREAVVY MAHTHDGARV 
       360        370        380        390        400
TMHCLWHGTT KDRKVIVKTM KSYIAKFAMG EYAHLVLLAA FDCIDDTKLV 
       410        420        430        440        450
KQIIISEMVS SLSEIISNKH GKKVLLYLLS PRDPAHLLPE IIQVLEKGDG 
       460        470        480        490        500
NAHSKKDVLI RRKELLEAAS PSLLNHLCEN AQSMVMDKSC CVVVSDILGS 
       510        520        530        540        550
AVGDLRPAME AVAALADGPL IPGGKDGQLH MAEHPAGHLV LKWLIEQDTK 
       560        570        580        590        600
MKDTEREERF SRILLEKVGL ENLKTWASVN RGAIILCCLL QSADESVAEE 
       610        620 
VKAMLKSSIP ELQRLQNSKG IEVLLEKLA
Length:629
Mass (Da):71,359
Last modified:January 20, 2016 - v2
<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:i73853BC76FC54523
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 are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
E9QJ83E9QJ83_DANRE
Pumilio homolog 3
pum3
601Annotation score:

Annotation score:1 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>
E9QFL4E9QFL4_DANRE
Pumilio homolog 3
pum3
186Annotation score:

Annotation score:1 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 Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti85D → A no nucleotide entry (PubMed:19319195).Curated1

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
CR628386 Genomic DNA No translation available.

NCBI Reference Sequences

More...RefSeqi		XP_003199363.1, XM_003199315.3

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSDART00000154037; ENSDARP00000129484; ENSDARG00000087779
ENSDART00000189109; ENSDARP00000153216; ENSDARG00000087779

Database of genes from NCBI RefSeq genomes

More...GeneIDi		553068

<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
CR628386 Genomic DNA No translation available.
RefSeqiXP_003199363.1, XM_003199315.3

3D structure databases

SMRiX1WGX5
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000129484

Proteomic databases

PaxDbiX1WGX5

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000154037; ENSDARP00000129484; ENSDARG00000087779
ENSDART00000189109; ENSDARP00000153216; ENSDARG00000087779
GeneIDi553068

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		9933
ZFINiZDB-GENE-030131-9808 pum3

Phylogenomic databases

eggNOGiKOG2050 Eukaryota
ENOG410XSHY LUCA
GeneTreeiENSGT00390000015757
OMAiYLQEHAQ
OrthoDBi845051at2759

Miscellaneous databases

Protein Ontology

More...PROi		PR:X1WGX5

Gene expression databases

BgeeiENSDARG00000087779 Expressed in 32 organ(s), highest expression level in presomitic mesoderm
ExpressionAtlasiX1WGX5 baseline

Family and domain databases

Gene3Di1.25.10.10, 1 hit
InterProiView protein in InterPro
IPR011989 ARM-like
IPR016024 ARM-type_fold
IPR012959 CPL_dom
IPR033133 PUM-HD
IPR040059 PUM3
IPR001313 Pumilio_RNA-bd_rpt
PANTHERiPTHR13389 PTHR13389, 1 hit
PfamiView protein in Pfam
PF08144 CPL, 1 hit
SMARTiView protein in SMART
SM00025 Pumilio, 6 hits
SUPFAMiSSF48371 SSF48371, 2 hits
PROSITEiView protein in PROSITE
PS50302 PUM, 5 hits
PS50303 PUM_HD, 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 nameiPUM3_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: X1WGX5
<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: January 20, 2016
Last sequence update: January 20, 2016
Last modified: May 8, 2019
This is version 38 of the entry and version 2 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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