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Entry version 61 (08 May 2019)
Sequence version 1 (03 May 2011)
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Protein

RNA-binding region-containing protein 3

Gene

rnpc3

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

Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprise less than 1% of all non-coding sequences.1 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

GO - Biological processi

<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 processmRNA processing, mRNA splicing

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-DRE-72165 mRNA Splicing - Minor Pathway

<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:
RNA-binding region-containing protein 31 Publication
Alternative name(s):
RNA-binding protein 40By similarity
<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:rnpc31 PublicationImported
<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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
<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 24

Organism-specific databases

Zebrafish Information Network genome database

More...
ZFINi
ZDB-GENE-060312-35 rnpc3

<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, Spliceosome

<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

Larval lethal with complete lethality by 10 days post-fertilization. Development of multiple organs is affected. Head, eye, lens, pancreas and liver are smaller than normal, and the swim bladder fails to inflate. The intestinal epithelium also remains thin and unfolded. U12-type introns are retained in mRNAs, whereas excision of U2-type introns is not affected. Assembly of both U12- and U11-containing snRNP complexes may be abnormal. Gene expression levels are broadly impacted; effects are not limited to U12-type intron-containing genes.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_00004427961 – 505RNA-binding region-containing protein 3Add BLAST505

Proteomic databases

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

More...
PaxDbi
F1Q8J0

<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 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

Widely expressed until 24 hours post-fertilization (hpf), probably due to inheritance of maternal transcripts. Expression becomes restricted to lens, pharyngeal region, liver/pancreas anlage and intestine at 48-72 hpf. Strongly expressed in pancreas and intestine at 96-120 hpf.1 Publication

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSDARG00000011247 Expressed in 30 organ(s), highest expression level in pharyngeal gill

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
F1Q8J0 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_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

Component of the U11/U12 snRNPs that are part of the U12-type spliceosome.

1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
7955.ENSDARP00000106976

<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
F1Q8J0

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_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>Domaini15 – 90RRM 1PROSITE-ProRule annotationAdd BLAST76
Domaini405 – 488RRM 2PROSITE-ProRule annotationAdd BLAST84

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 biasi183 – 215Pro-richPROSITE-ProRule annotationAdd BLAST33

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG4206 Eukaryota
ENOG410XQEY LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00530000063786

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000007217

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
F1Q8J0

KEGG Orthology (KO)

More...
KOi
K13157

Identification of Orthologs from Complete Genome Data

More...
OMAi
RQRMNKL

Database of Orthologous Groups

More...
OrthoDBi
1080666at2759

TreeFam database of animal gene trees

More...
TreeFami
TF324298

Family and domain databases

Conserved Domains Database

More...
CDDi
cd12238 RRM1_RBM40_like, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.70.330, 2 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR034147 RBM40_RRM1
IPR000504 RRM_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00076 RRM_1, 2 hits

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00360 RRM, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF54928 SSF54928, 2 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50102 RRM, 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>. 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>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

F1Q8J0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAETDEADVQ TKKSKTLIIR HLPRELSRDE KEDLLKYFGA SSVRVLSEKG
60 70 80 90 100
PLKHMAFATF SSETSASKAL NRLHQLRILG RTLVVEFAKD QDSASILKDP
110 120 130 140 150
PVSDRTAAAV AEKEKKEKQQ PSVPLMDTSI APSLGLKFQT NPTLKYLYPP
160 170 180 190 200
PSSGILTNIT HTLLSVPKFY VQVLHLMNKM NLPSPFRPVT APPPMFEMPS
210 220 230 240 250
GPLPPPFPPE NPPLPEHDES GSEEESEYES EDEEERERMI RLMGLVNQPC
260 270 280 290 300
KRPLRTKTSS KRKKPKLKDL LFIPKPDSHG PSGPVLQPAD VFEQPHALGQ
310 320 330 340 350
KKIEFHISSE VSAILEGPGQ NQKLPFADAT EDTPDMEVSA QETTEGFGKI
360 370 380 390 400
YPSAQVPRQE EEQEEDEDIP SEFISRRELE RGRLSRDEIK KLSVFKKYEP
410 420 430 440 450
GEPTCRLYVK NVAKHVEEKD LKFIYGRYID ISSEEERNMF DIVLMKEGRM
460 470 480 490 500
KGQAFIGLPS ERSAQKALKE TNGYVLKDKP LVVQFARSAK PKQESADPKK

GGRKH
Length:505
Mass (Da):56,943
Last modified:May 3, 2011 - 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:i47DCE302AE06E006
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
X1WCA8X1WCA8_DANRE
RNA-binding region-containing prote...
rnpc3
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 conflicti96I → V in AAI14289 (Ref. 2) Curated1
Sequence conflicti231E → G in AAI14289 (Ref. 2) Curated1
Sequence conflicti258T → I in AAI14289 (Ref. 2) 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
CT961047 Genomic DNA No translation available.
BC114288 mRNA Translation: AAI14289.1

NCBI Reference Sequences

More...
RefSeqi
NP_001035019.1, NM_001039930.1
XP_005162876.1, XM_005162819.3
XP_005162877.1, XM_005162820.2
XP_005162878.1, XM_005162821.3

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSDART00000017427; ENSDARP00000019728; ENSDARG00000011247
ENSDART00000183580; ENSDARP00000155505; ENSDARG00000011247
ENSDART00000185020; ENSDARP00000155778; ENSDARG00000011247

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
565672

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
dre:565672

<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
CT961047 Genomic DNA No translation available.
BC114288 mRNA Translation: AAI14289.1
RefSeqiNP_001035019.1, NM_001039930.1
XP_005162876.1, XM_005162819.3
XP_005162877.1, XM_005162820.2
XP_005162878.1, XM_005162821.3

3D structure databases

SMRiF1Q8J0
ModBaseiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000106976

Proteomic databases

PaxDbiF1Q8J0

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000017427; ENSDARP00000019728; ENSDARG00000011247
ENSDART00000183580; ENSDARP00000155505; ENSDARG00000011247
ENSDART00000185020; ENSDARP00000155778; ENSDARG00000011247
GeneIDi565672
KEGGidre:565672

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
55599
ZFINiZDB-GENE-060312-35 rnpc3

Phylogenomic databases

eggNOGiKOG4206 Eukaryota
ENOG410XQEY LUCA
GeneTreeiENSGT00530000063786
HOGENOMiHOG000007217
InParanoidiF1Q8J0
KOiK13157
OMAiRQRMNKL
OrthoDBi1080666at2759
TreeFamiTF324298

Enzyme and pathway databases

ReactomeiR-DRE-72165 mRNA Splicing - Minor Pathway

Miscellaneous databases

Protein Ontology

More...
PROi
PR:F1Q8J0

Gene expression databases

BgeeiENSDARG00000011247 Expressed in 30 organ(s), highest expression level in pharyngeal gill
ExpressionAtlasiF1Q8J0 baseline

Family and domain databases

CDDicd12238 RRM1_RBM40_like, 1 hit
Gene3Di3.30.70.330, 2 hits
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR034147 RBM40_RRM1
IPR000504 RRM_dom
PfamiView protein in Pfam
PF00076 RRM_1, 2 hits
SMARTiView protein in SMART
SM00360 RRM, 2 hits
SUPFAMiSSF54928 SSF54928, 2 hits
PROSITEiView protein in PROSITE
PS50102 RRM, 2 hits

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 nameiRNPC3_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: F1Q8J0
Secondary accession number(s): Q29RB3
<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 31, 2018
Last sequence update: May 3, 2011
Last modified: May 8, 2019
This is version 61 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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