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UniProtKB - Q7T3C6 (CPSF5_DANRE)

Entry version 105 (02 Dec 2020)
Sequence version 1 (01 Oct 2003)
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Protein

Cleavage and polyadenylation specificity factor subunit 5

Gene

nudt21

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

Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs. CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation. The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs. Binds to 5'-UGUA-3' elements localized upstream of pA signals that act as enhancers of pre-mRNA 3'-end processing. The homodimer mediates simultaneous sequence-specific recognition of two 5'-UGUA-3' elements within the pre-mRNA. Plays a role in somatic cell fate transitions and pluripotency by regulating widespread changes in gene expression through an APA-dependent function. Binds to chromatin. Binds to, but does not hydrolyze mono- and di-adenosine nucleotides.By similarity

Caution

Lacks the conserved metal-binding residues in the NUDIX motif and is not expected to have hydrolase activity.Curated

<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 functionRNA-binding
Biological processDifferentiation, mRNA processing

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-DRE-72163, mRNA Splicing - Major Pathway
R-DRE-72187, mRNA 3'-end processing
R-DRE-73856, RNA Polymerase II Transcription Termination
R-DRE-77595, Processing of Intronless Pre-mRNAs

<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:
Cleavage and polyadenylation specificity factor subunit 5By similarity
Alternative name(s):
Nudix hydrolase 21By similarity
<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:nudt21By similarity
Synonyms:cpsf5By similarity
<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>OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
<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 identifieri7955 [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 › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Danionidae › Danioninae › Danio
<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
  • UP000000437 <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 18

Organism-specific databases

Zebrafish Information Network genome database

More...ZFINi		ZDB-GENE-040426-1316, nudt21

<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

Cytoplasm, 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_00000571541 – 228Cleavage and polyadenylation specificity factor subunit 5Add BLAST228

Proteomic databases

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

More...PaxDbi		Q7T3C6

<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		ENSDARG00000003153, Expressed in gastrula and 35 other tissues

ExpressionAtlas, Differential and Baseline Expression

More...ExpressionAtlasi		Q7T3C6, 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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer (via N- and C-terminus); binds RNA as homodimer.

Component of the cleavage factor Im (CFIm) complex.

By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei56Interaction with RNABy similarity1
Sitei64Interaction with RNABy similarity1

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		7955.ENSDARP00000017229

<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		Q7T3C6

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%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>Domaini77 – 202Nudix hydrolasePROSITE-ProRule annotationAdd BLAST126

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni103 – 105Interaction with RNABy similarity3

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>Motifi110 – 131Nudix boxAdd BLAST22

<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 Nudix hydrolase family. CPSF5 subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG1689, Eukaryota

Ensembl GeneTree

More...GeneTreei		ENSGT00390000015814

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_068704_2_1_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q7T3C6

Identification of Orthologs from Complete Genome Data

More...OMAi		EWEIGDC

Database of Orthologous Groups

More...OrthoDBi		1194206at2759

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q7T3C6

TreeFam database of animal gene trees

More...TreeFami		TF106356

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR016706, Cleav_polyA_spec_factor_su5
IPR015797, NUDIX_hydrolase-like_dom_sf
IPR000086, NUDIX_hydrolase_dom

The PANTHER Classification System

More...PANTHERi		PTHR13047, PTHR13047, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF13869, NUDIX_2, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF017888, CPSF-25, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF55811, SSF55811, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51462, NUDIX, 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.

Q7T3C6-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSVVPPNRSS TGWPRGVNQF GNKYITQATK PLTLERTINL YPLTNYTFGT 
        60         70         80         90        100
KEPLYEKDSS VAARFQRMRE EFEKIGMRRT VEGVLIVHEH RLPHVLLLQL 
       110        120        130        140        150
GTTFFKLPGG ELNPGEDEVE GLKRLMTEIL GRQDGVKQDW VIDDCIGNWW 
       160        170        180        190        200
RPNFEPPQYP YIPAHITKPK EHKKLFLVQL QEKALFAVPK NYKLVAAPLF 
       210        220 
ELYDNAPGYG PIISSLPQLL SRFNFIYN
Length:228
Mass (Da):26,272
Last modified:October 1, 2003 - 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:i3ADFD7E8CB397C4D
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
BC053172 mRNA Translation: AAH53172.1

NCBI Reference Sequences

More...RefSeqi		NP_957411.1, NM_201117.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSDART00000023721; ENSDARP00000017229; ENSDARG00000003153

Database of genes from NCBI RefSeq genomes

More...GeneIDi		394092

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		dre:394092

<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
BC053172 mRNA Translation: AAH53172.1
RefSeqiNP_957411.1, NM_201117.1

3D structure databases

SMRiQ7T3C6
ModBaseiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000017229

Proteomic databases

PaxDbiQ7T3C6

Genome annotation databases

EnsembliENSDART00000023721; ENSDARP00000017229; ENSDARG00000003153
GeneIDi394092
KEGGidre:394092

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		11051
ZFINiZDB-GENE-040426-1316, nudt21

Phylogenomic databases

eggNOGiKOG1689, Eukaryota
GeneTreeiENSGT00390000015814
HOGENOMiCLU_068704_2_1_1
InParanoidiQ7T3C6
OMAiEWEIGDC
OrthoDBi1194206at2759
PhylomeDBiQ7T3C6
TreeFamiTF106356

Enzyme and pathway databases

ReactomeiR-DRE-72163, mRNA Splicing - Major Pathway
R-DRE-72187, mRNA 3'-end processing
R-DRE-73856, RNA Polymerase II Transcription Termination
R-DRE-77595, Processing of Intronless Pre-mRNAs

Miscellaneous databases

Protein Ontology

More...PROi		PR:Q7T3C6

Gene expression databases

BgeeiENSDARG00000003153, Expressed in gastrula and 35 other tissues
ExpressionAtlasiQ7T3C6, baseline

Family and domain databases

InterProiView protein in InterPro
IPR016706, Cleav_polyA_spec_factor_su5
IPR015797, NUDIX_hydrolase-like_dom_sf
IPR000086, NUDIX_hydrolase_dom
PANTHERiPTHR13047, PTHR13047, 1 hit
PfamiView protein in Pfam
PF13869, NUDIX_2, 1 hit
PIRSFiPIRSF017888, CPSF-25, 1 hit
SUPFAMiSSF55811, SSF55811, 1 hit
PROSITEiView protein in PROSITE
PS51462, NUDIX, 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 nameiCPSF5_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: Q7T3C6
<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 7, 2006
Last sequence update: October 1, 2003
Last modified: December 2, 2020
This is version 105 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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