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Entry version 102 (07 Oct 2020)
Sequence version 1 (01 Mar 2002)
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Protein

Single-strand DNA endonuclease 1

Gene

SEND1

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score:

Annotation score:3 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

Single-stranded DNA endonuclease activity in vitro (PubMed:12602891). May not be active as double-stranded DNA endonuclease (PubMed:12602891). Endonuclease which cleaves flap structures at the junction between single-stranded DNA and double-stranded DNA with a specific cleavage site in the 5' overhang strand exactly one nucleotide 3' of the branch point (By similarity). Structure- and sequence-specific nuclease that resolves holliday junctions (HJs) by symmetrically oriented incisions in two opposing strands near the junction point, thus leading to ligatable products; HJs are physical links between homologous DNA molecules that arise as central intermediary structures during homologous recombination and repair in meiotic and somatic cells (By similarity). Probably involved in the resolution of toxic replication structures to ensure genome stability, and to maintain telomere integrity and replication (By similarity).By similarity1 Publication

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+By similarityNote: Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi30Magnesium 1By similarity1
Metal bindingi76Magnesium 1By similarity1
Metal bindingi144Magnesium 1By similarity1
Metal bindingi146Magnesium 1By similarity1
Metal bindingi165Magnesium 2By similarity1
Metal bindingi167Magnesium 2By similarity1
Metal bindingi217Magnesium 2By similarity1

<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 functionEndonuclease, Hydrolase, Nuclease
Biological processDNA damage, DNA repair
LigandMagnesium, Metal-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%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:
Single-strand DNA endonuclease 11 Publication (EC:3.1.-.-)
Short name:
OsSEND-11 Publication
Alternative name(s):
Flap endonuclease GEN-like 2Curated
Short name:
XPG-like endonuclease 2Curated
<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:SEND11 Publication
Synonyms:GEN2
Ordered Locus Names:Os08g0101600Curated, LOC_Os08g01130Curated
ORF Names:B1147B12.17, OsJ_25722Imported
<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
  • UP000007752 <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 8
  • UP000059680 Componenti: Chromosome 8
  • UP000000763 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

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_00003156251 – 641Single-strand DNA endonuclease 1Add BLAST641

Proteomic databases

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

More...
PaxDbi
Q8W5R1

PRoteomics IDEntifications database

More...
PRIDEi
Q8W5R1

<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

Highly expressed in shoot apical meristem (SAM) and young leaves. Expressed in roots, flag leaf and panicles.1 Publication

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

By the DNA-damaging agents methyl methanesulfonate (MMS), H2O2 and UV. Down-regulated by sucrose starvation and the cell cycle inhibitors aphidicolin, hydroxyurea and colchicine.1 Publication

<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.OS08T0101600-01

<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
Q8W5R1

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

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>Regioni1 – 90N-domainAdd BLAST90
Regioni2 – 97XPG-N domainBy similarityAdd BLAST96
Regioni132 – 221I-domainAdd BLAST90
Regioni132 – 220I-domainBy similarityAdd BLAST89
Regioni132 – 217XPG-I domainBy similarityAdd BLAST86
Regioni217 – 3505'-3' exonuclease domainBy similarityAdd BLAST134

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2519, Eukaryota

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q8W5R1

KEGG Orthology (KO)

More...
KOi
K15338

Database of Orthologous Groups

More...
OrthoDBi
1094524at2759

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR036279, 5-3_exonuclease_C_sf
IPR008918, HhH2
IPR029060, PIN-like_dom_sf
IPR006086, XPG-I_dom
IPR006084, XPG/Rad2
IPR006085, XPG_DNA_repair_N

The PANTHER Classification System

More...
PANTHERi
PTHR11081, PTHR11081, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00867, XPG_I, 1 hit
PF00752, XPG_N, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00853, XPGRADSUPER

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00279, HhH2, 1 hit
SM00484, XPGI, 1 hit
SM00485, XPGN, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF47807, SSF47807, 1 hit
SSF88723, SSF88723, 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>Sequence (1+)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 has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q8W5R1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MGVKNLWDIL ESCKKKLPLH HLQNKKVCVD LSCWLVQMYS ANRSPAFAKD
60 70 80 90 100
KVYLKNLFHR IRALLALNCT LLFVTDGAIP SLKLATYRRR LGSISHAAKE
110 120 130 140 150
SDQPNSHPSI SLRRNKGSEF SCMIKEAKRL GMALGIPCLD GLEEAEAQCA
160 170 180 190 200
SLDLESLCDG CFTSDSDAFL FGARTVYRDV FIGEGGYVIC YEMEDIEKTL
210 220 230 240 250
GFGRNSLISL AVLLGSDYSN GVNGFGPETA CRLVKSVGDN LILDQILSNG
260 270 280 290 300
VKATRKCKGK NSGNKVDDMC PKASSCEVGM TQDSDGQFRD VINAYLEPKC
310 320 330 340 350
HSPDSEAVQR VCGQHPFLRP QLQKICEEYF DWSPEKTDQY ILPKIAEREL
360 370 380 390 400
RRFSDLRSAS SALGIKPLLS EIPVPCPVLA IVKQRKVHGN ECYEVSWRNI
410 420 430 440 450
EGLQVSVVPG DLVKSACPEK ITEFLEKKGE EKKQKRRARP KKSGQAAVKD
460 470 480 490 500
VDEQLQELLL GIEADSGGIL GATASVCQTL TAAYTVAVED VVDLSSPSPP
510 520 530 540 550
LRKLSKSQKK MMAEDVNVAG MNMNKMESES SFSTQSSTSD VDNQLIDLSS
560 570 580 590 600
PLAGGDNGMK GGRRALADIS NVGSHSTETD GGGGGGGGVA SVGHGTTIDL
610 620 630 640
SSPSPAIGDR SRVHHDDDDV IHERKARDLR MFLDSIRNEL Y
Length:641
Mass (Da):69,918
Last modified:March 1, 2002 - 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:i6FECE8642BEA981A
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
A0A0P0XAS5A0A0P0XAS5_ORYSJ
Os08g0101600 protein
Os08g0101600, OSNPB_080101600
112Annotation 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>

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
AB074260 mRNA Translation: BAB72003.1
AP008214 Genomic DNA Translation: BAF22676.1
AP014964 Genomic DNA No translation available.
CM000145 Genomic DNA Translation: EEE67892.1

NCBI Reference Sequences

More...
RefSeqi
XP_015650609.1, XM_015795123.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
4344420

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
osa:4344420

<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
AB074260 mRNA Translation: BAB72003.1
AP008214 Genomic DNA Translation: BAF22676.1
AP014964 Genomic DNA No translation available.
CM000145 Genomic DNA Translation: EEE67892.1
RefSeqiXP_015650609.1, XM_015795123.1

3D structure databases

SMRiQ8W5R1
ModBaseiSearch...

Protein-protein interaction databases

STRINGi4530.OS08T0101600-01

Proteomic databases

PaxDbiQ8W5R1
PRIDEiQ8W5R1

Genome annotation databases

GeneIDi4344420
KEGGiosa:4344420

Phylogenomic databases

eggNOGiKOG2519, Eukaryota
InParanoidiQ8W5R1
KOiK15338
OrthoDBi1094524at2759

Family and domain databases

InterProiView protein in InterPro
IPR036279, 5-3_exonuclease_C_sf
IPR008918, HhH2
IPR029060, PIN-like_dom_sf
IPR006086, XPG-I_dom
IPR006084, XPG/Rad2
IPR006085, XPG_DNA_repair_N
PANTHERiPTHR11081, PTHR11081, 1 hit
PfamiView protein in Pfam
PF00867, XPG_I, 1 hit
PF00752, XPG_N, 1 hit
PRINTSiPR00853, XPGRADSUPER
SMARTiView protein in SMART
SM00279, HhH2, 1 hit
SM00484, XPGI, 1 hit
SM00485, XPGN, 1 hit
SUPFAMiSSF47807, SSF47807, 1 hit
SSF88723, SSF88723, 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 nameiGENL2_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: Q8W5R1
Secondary accession number(s): B9FYM5
<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: January 15, 2008
Last sequence update: March 1, 2002
Last modified: October 7, 2020
This is version 102 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

Reference proteome

Documents

  1. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  2. SIMILARITY comments
    Index of protein domains and families
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