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Entry version 90 (31 Jul 2019)
Sequence version 1 (01 Jun 2003)
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Protein

Zinc finger CCCH domain-containing protein 56

Gene

Os08g0159800

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-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>
-Protein predictedi <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 <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri87 – 114C3H1-type 1PROSITE-ProRule annotationAdd BLAST28
Zinc fingeri169 – 197C3H1-type 2PROSITE-ProRule annotationAdd BLAST29
Zinc fingeri245 – 273C3H1-type 3PROSITE-ProRule annotationAdd BLAST29

<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 functionDNA-binding
LigandMetal-binding, Zinc

<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:
Zinc finger CCCH domain-containing protein 56
Short name:
OsC3H56
<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
Ordered Locus Names:Os08g0159800, LOC_Os08g06330
ORF Names:P0498E12.129, P0672D01.112
<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>OrganismiOryza sativa subsp. japonica (Rice)
<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 identifieri39947 [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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
<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
  • UP000059680 <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 8

<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

<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_00003468491 – 367Zinc finger CCCH domain-containing protein 56Add BLAST367

Proteomic databases

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

More...
PaxDbi
Q84UQ3

PRoteomics IDEntifications database

More...
PRIDEi
Q84UQ3

<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

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q84UQ3 OS

<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
4530.OS08T0159800-00

<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

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 biasi67 – 75Poly-Gly9
Compositional biasi157 – 167Poly-GlyAdd BLAST11
Compositional biasi213 – 219Poly-Gly7
Compositional biasi224 – 235Poly-AlaAdd BLAST12

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri87 – 114C3H1-type 1PROSITE-ProRule annotationAdd BLAST28
Zinc fingeri169 – 197C3H1-type 2PROSITE-ProRule annotationAdd BLAST29
Zinc fingeri245 – 273C3H1-type 3PROSITE-ProRule annotationAdd BLAST29

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG1677 Eukaryota
COG5063 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000242590

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q84UQ3

Identification of Orthologs from Complete Genome Data

More...
OMAi
QGGVPSK

Database of Orthologous Groups

More...
OrthoDBi
883647at2759

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR041367 Znf-CCCH_4
IPR000571 Znf_CCCH
IPR036855 Znf_CCCH_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00642 zf-CCCH, 2 hits
PF18044 zf-CCCH_4, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00356 ZnF_C3H1, 3 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF90229 SSF90229, 3 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50103 ZF_C3H1, 3 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>Sequencei

<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.

Q84UQ3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDYTNAIHII PDAAGPDAWA NAAAQGGDAG IWATEDDYNS QWNADGGGGG
60 70 80 90 100
SSRAGSEQPP PGKKSRGGGG GEGGGNTSKS RAIGKMFFKT KLCCKFRAGT
110 120 130 140 150
CPYVTNCNFA HGMEELRKPP PNWQEIVAAH EEATEAREEH QIPIMTSSGP
160 170 180 190 200
TAGGDAGCGG GGGGGSGRAY KGRHCKKFYT DEGCPYGDAC TFLHDEQSKA
210 220 230 240 250
RESVAISLSP SVGGGGGGGS YNSAAAAAAS ASAAAGNGPM QKPSNWKTRI
260 270 280 290 300
CNKWEMTGYC PFGSKCHFAH GAAELHKYGG GLVDIDSRDA AATPDSKQAV
310 320 330 340 350
VSAKAPAETA AASTTVLPHA DVYHLGVQAQ RSTIAGQRSG QVQRPIQKWK
360
GPDKISRIYG DWIDETE
Length:367
Mass (Da):37,958
Last modified:June 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:iE08588C319690D98
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
AP004635 Genomic DNA Translation: BAC66728.1
AP004698 Genomic DNA Translation: BAC99662.1
AP008214 Genomic DNA Translation: BAF22958.1
AP014964 Genomic DNA Translation: BAT03925.1

NCBI Reference Sequences

More...
RefSeqi
XP_015648128.1, XM_015792642.1
XP_015648129.1, XM_015792643.1

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
Os08t0159800-00; Os08t0159800-00; Os08g0159800

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
4344715

Gramene; a comparative resource for plants

More...
Gramenei
Os08t0159800-00; Os08t0159800-00; Os08g0159800

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
osa:4344715

<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
AP004635 Genomic DNA Translation: BAC66728.1
AP004698 Genomic DNA Translation: BAC99662.1
AP008214 Genomic DNA Translation: BAF22958.1
AP014964 Genomic DNA Translation: BAT03925.1
RefSeqiXP_015648128.1, XM_015792642.1
XP_015648129.1, XM_015792643.1

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

STRINGi4530.OS08T0159800-00

Proteomic databases

PaxDbiQ84UQ3
PRIDEiQ84UQ3

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOs08t0159800-00; Os08t0159800-00; Os08g0159800
GeneIDi4344715
GrameneiOs08t0159800-00; Os08t0159800-00; Os08g0159800
KEGGiosa:4344715

Phylogenomic databases

eggNOGiKOG1677 Eukaryota
COG5063 LUCA
HOGENOMiHOG000242590
InParanoidiQ84UQ3
OMAiQGGVPSK
OrthoDBi883647at2759

Gene expression databases

GenevisibleiQ84UQ3 OS

Family and domain databases

InterProiView protein in InterPro
IPR041367 Znf-CCCH_4
IPR000571 Znf_CCCH
IPR036855 Znf_CCCH_sf
PfamiView protein in Pfam
PF00642 zf-CCCH, 2 hits
PF18044 zf-CCCH_4, 1 hit
SMARTiView protein in SMART
SM00356 ZnF_C3H1, 3 hits
SUPFAMiSSF90229 SSF90229, 3 hits
PROSITEiView protein in PROSITE
PS50103 ZF_C3H1, 3 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 nameiC3H56_ORYSJ
<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: Q84UQ3
Secondary accession number(s): A0A0P0XC61
<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: September 2, 2008
Last sequence update: June 1, 2003
Last modified: July 31, 2019
This is version 90 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

Complete proteome, Reference proteome

Documents

  1. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
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