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Entry version 130 (26 Feb 2020)
Sequence version 3 (16 Jun 2009)
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Protein

B3 domain-containing protein VP1

Gene

VP1

Organism
Oryza sativa subsp. japonica (Rice)
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 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

Probable transcription factor that may participate in abscisic acid-regulated gene expression during seed development. May be required for seed maturation and dormancy induction.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> 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 bindingi537 – 638TF-B3PROSITE-ProRule annotationAdd BLAST102

<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 functionActivator, Developmental protein, DNA-binding
Biological processAbscisic acid signaling pathway, Transcription, Transcription regulation

<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:
B3 domain-containing protein VP1
Short name:
OsVP1
Alternative name(s):
Protein viviparous homolog
<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:VP1
Ordered Locus Names:Os01g0911700, LOC_Os01g68370
ORF Names:P0470A12.15-1, P0470A12.15-2
<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>OrganismiOryza sativa subsp. japonica (Rice)
<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 identifieri39947 [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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
<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
  • UP000059680 <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 1
  • UP000000763 Componenti: Chromosome 1

<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

Keywords - Cellular componenti

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_00001115291 – 727B3 domain-containing protein VP1Add BLAST727

Proteomic databases

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

More...
PaxDbi
P37398

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P37398

<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

Expressed in the whole embryo from 2 to 4 days after pollination (DAP). At 6 DAP, expressed in the regions where the shoot and radicle are developing, and in the aleurone layers and the outermost cell layers of the endosperm. Later, in the embryo development, expressed in vascular tissue, coleoptile, leaf, shoot meristem, radicle, scutellum and epiblast. In mature embryo (20 DAP), expression levels decrease.1 Publication

Gene expression databases

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
P37398 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

<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

Interacts with RAD23 (PubMed:9225866).

Interacts (via N-terminus) with TRAB1 (PubMed:10611387).

Interacts with ABI5 (PubMed:17604002).

3 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
4530.OS01T0911700-02

<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
P37398

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

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 biasi20 – 30Poly-GlyAdd BLAST11
Compositional biasi71 – 80Poly-Ser10
Compositional biasi683 – 691Poly-Ala9

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG410IJ7Z Eukaryota
ENOG4111P6C LUCA

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P37398

Identification of Orthologs from Complete Genome Data

More...
OMAi
GGNMAWP

Database of Orthologous Groups

More...
OrthoDBi
317013at2759

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.40.330.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003340 B3_DNA-bd
IPR015300 DNA-bd_pseudobarrel_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02362 B3, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01019 B3, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF101936 SSF101936, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50863 B3, 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>Sequences (2)i

<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.

This entry describes 2 <p>This subsection of the 'Sequence' section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform. This section is only present in reviewed entries, i.e. in UniProtKB/Swiss-Prot.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: P37398-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MDASAGSSAP HSHGNPGKQG GGGGGGGGRG KAPAAEIRGE AARDDVFFAD
60 70 80 90 100
DTFPLLPDFP CLSSPSSSTF SSSSSSNSSS AFTTAAGGGC GGEPSEPASA
110 120 130 140 150
ADGFGELADI DQLLDLASLS VPWEAEQPLF PDDVGMMIED AMSGQPHQAD
160 170 180 190 200
DCTGDGDTKA VMEAAGGGDD AGDACMEGSD APDDLPAFFM EWLTSNREYI
210 220 230 240 250
SADDLRSIRL RRSTIEAAAA RLGGGRQGTM QLLKLILTWV QNHHLQKKRP
260 270 280 290 300
RTAIDDGAAS SDPQLPSPGA NPGYEFPSGG QEMGSAAATS WMPYQAFTPP
310 320 330 340 350
AAYGGDAMYP GAAGPFPFQQ SCSKSSVVVS SQPFSPPTAA AAGDMHASGG
360 370 380 390 400
GNMAWPQQFA PFPVSSTSSY TMPSVVPPPF TAGFPGQYSG GHAMCSPRLA
410 420 430 440 450
GVEPSSTKEA RKKRMARQRR LSCLQQQRSQ QLNLSQIHIS GHPQEPSPRA
460 470 480 490 500
AHSAPVTPSS AGCRSWGIWP PAAQIIQNPL SNKPNPPPAT SKQPKPSPEK
510 520 530 540 550
PKPKPQAAAT AGAESLQRST ASEKRQAKTD KNLRFLLQKV LKQSDVGSLG
560 570 580 590 600
RIVLPKEAEV HLPELKTRDG VSIPMEDIGT SQVWNMRYRF WPNNKSRMYL
610 620 630 640 650
LENTGDFVRS NELQEGDFIV IYSDIKSGKY LIRGVKVRRA AQEQGNSSGA
660 670 680 690 700
VGKHKHGSPE KPGVSSNTKA AGAEDGTGGD DSAEAAAAAA AGKADGGGCK
710 720
GKSPHGVRRS RQEAAAAASM SQMAVSI
Length:727
Mass (Da):75,802
Last modified:June 16, 2009 - v3
<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:i563C2FD5D8FF8160
GO
Isoform 2 (identifier: P37398-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     9-31: Missing.

Show »
Length:704
Mass (Da):73,836
Checksum:i17872EC56F9795DA
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence BAA04066 differs from that shown. Reason: Erroneous gene model prediction.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_0195849 – 31Missing in isoform 2. 1 PublicationAdd BLAST23

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
D16640 Genomic DNA Translation: BAA04066.1 Sequence problems.
AP003436 Genomic DNA Translation: BAD82432.1
AP003436 Genomic DNA Translation: BAD82433.1
AP008207 Genomic DNA Translation: BAF07076.2
AP014957 Genomic DNA Translation: BAS75841.1
AP014957 Genomic DNA Translation: BAS75842.1
AK073805 mRNA Translation: BAG93647.1
AK105441 mRNA No translation available.

NCBI Reference Sequences

More...
RefSeqi
XP_015629318.1, XM_015773832.1 [P37398-1]

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
Os01t0911700-01; Os01t0911700-01; Os01g0911700 [P37398-2]
Os01t0911700-02; Os01t0911700-02; Os01g0911700 [P37398-1]

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
4324314

Gramene; a comparative resource for plants

More...
Gramenei
Os01t0911700-01; Os01t0911700-01; Os01g0911700 [P37398-2]
Os01t0911700-02; Os01t0911700-02; Os01g0911700 [P37398-1]

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
osa:4324314

Keywords - Coding sequence diversityi

Alternative splicing

<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
D16640 Genomic DNA Translation: BAA04066.1 Sequence problems.
AP003436 Genomic DNA Translation: BAD82432.1
AP003436 Genomic DNA Translation: BAD82433.1
AP008207 Genomic DNA Translation: BAF07076.2
AP014957 Genomic DNA Translation: BAS75841.1
AP014957 Genomic DNA Translation: BAS75842.1
AK073805 mRNA Translation: BAG93647.1
AK105441 mRNA No translation available.
RefSeqiXP_015629318.1, XM_015773832.1 [P37398-1]

3D structure databases

SMRiP37398
ModBaseiSearch...

Protein-protein interaction databases

STRINGi4530.OS01T0911700-02

PTM databases

iPTMnetiP37398

Proteomic databases

PaxDbiP37398

Genome annotation databases

EnsemblPlantsiOs01t0911700-01; Os01t0911700-01; Os01g0911700 [P37398-2]
Os01t0911700-02; Os01t0911700-02; Os01g0911700 [P37398-1]
GeneIDi4324314
GrameneiOs01t0911700-01; Os01t0911700-01; Os01g0911700 [P37398-2]
Os01t0911700-02; Os01t0911700-02; Os01g0911700 [P37398-1]
KEGGiosa:4324314

Phylogenomic databases

eggNOGiENOG410IJ7Z Eukaryota
ENOG4111P6C LUCA
InParanoidiP37398
OMAiGGNMAWP
OrthoDBi317013at2759

Gene expression databases

GenevisibleiP37398 OS

Family and domain databases

Gene3Di2.40.330.10, 1 hit
InterProiView protein in InterPro
IPR003340 B3_DNA-bd
IPR015300 DNA-bd_pseudobarrel_sf
PfamiView protein in Pfam
PF02362 B3, 1 hit
SMARTiView protein in SMART
SM01019 B3, 1 hit
SUPFAMiSSF101936 SSF101936, 1 hit
PROSITEiView protein in PROSITE
PS50863 B3, 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 nameiVIV_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: P37398
Secondary accession number(s): A0A0P0VBZ7
, B7EMQ0, Q0JGQ2, Q5N7W1, Q5N7W2
<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: October 1, 1994
Last sequence update: June 16, 2009
Last modified: February 26, 2020
This is version 130 of the entry and version 3 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

Reference proteome

Documents

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