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Entry version 101 (02 Dec 2020)
Sequence version 1 (05 Jul 2004)
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Protein

Lysine-specific histone demethylase 1 homolog 2

Gene

Os08g0143400

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>
-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

Probable histone demethylase.By similarity

<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

FADCurated

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei192FADBy similarity1
Binding sitei194FADBy similarity1
Binding sitei200FADBy similarity1
Binding sitei571FADBy 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

  • oxidoreductase activity Source: GO_Central

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 functionChromatin regulator, Oxidoreductase
LigandFAD, Flavoprotein

<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:
Lysine-specific histone demethylase 1 homolog 2 (EC:1.-.-.-)
Alternative name(s):
Flavin-containing amine oxidase domain-containing protein 2
Protein LSD1-LIKE 2
<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
Ordered Locus Names:Os08g0143400, LOC_Os08g04780
ORF Names:P0025F03.17-1, P0025F03.17-2, P0473D02.39-1, P0473D02.39-2
<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 8
  • UP000000763 Componenti: Chromosome 8

<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_00003428971 – 763Lysine-specific histone demethylase 1 homolog 2Add BLAST763

Proteomic databases

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

More...
PaxDbi
Q6YYZ1

PRoteomics IDEntifications database

More...
PRIDEi
Q6YYZ1

<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

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q6YYZ1, baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q6YYZ1, 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.OS08T0143400-01

<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
Q6YYZ1

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>Domaini53 – 152SWIRMPROSITE-ProRule annotationAdd BLAST100

<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 flavin monoamine oxidase family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG0029, Eukaryota

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q6YYZ1

Identification of Orthologs from Complete Genome Data

More...
OMAi
FFVTRWS

Database of Orthologous Groups

More...
OrthoDBi
1034142at2759

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.10.10, 1 hit
3.50.50.60, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002937, Amino_oxidase
IPR036188, FAD/NAD-bd_sf
IPR009057, Homeobox-like_sf
IPR007526, SWIRM
IPR036388, WH-like_DNA-bd_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01593, Amino_oxidase, 1 hit
PF04433, SWIRM, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF46689, SSF46689, 1 hit
SSF51905, SSF51905, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50934, SWIRM, 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

Q6YYZ1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSSSSRRPAR RAALTARSSY DESLVDAELE SYLGNARSRR ISRLRRLSAD
60 70 80 90 100
ERQRETETEA LIALSLGFPI DELLPAERPL LPAPVAAAPN DYIVVRNHIL
110 120 130 140 150
ASWRADPRVP LPRSRVQETV AASYDNLVAV AHGFLAREGH INFGVSAAFP
160 170 180 190 200
ASPPPDAPQR LAASVLVVGA GLAGLAAARQ LLRFGLRVLV LEGRARPGGR
210 220 230 240 250
VYTTHLGGDQ AAVELGGSVI TGIHTNPLGV LARQLGIPLH KVRDSCPLYH
260 270 280 290 300
HDGRTVDMKL DRSMDLVFNT LLEHATRLRE YLKKAAEGIS LGEGIERLRR
310 320 330 340 350
FYKVAKSVEE REVLDWHLAN LEFSNAGCLS ELSLAHWDQD DQYEMGGDHC
360 370 380 390 400
FLAGGNARLV HALCDGVPVL YEKTVKRIEH GEDGVSITVE GGQVFKADMA
410 420 430 440 450
LCTAPLGVLK SRSIIFEPEL PERKLEAIQR LGFGLLNKVA MVFPHVFWDE
460 470 480 490 500
EIDTFGCLNK ERSKRGEFFL FYSYHTVSGG AVLIALVAGE AALEFEKVDP
510 520 530 540 550
AVALHRVLGI LKGIYGPKGV TVPDPIQSCC TRWGSDPLCS GSYSHIRVGS
560 570 580 590 600
SGTDYDILAE SVNDRLFFAG EATNRAYPAT MHGALLSGLR EASKILHASE
610 620 630 640 650
SRLNSDYKKY ALQKSIRLIN NVLDDLFMEP DLECGRFSFV FSYITPEEEQ
660 670 680 690 700
APGLARITLE KPLLLPSKKR KVKGNQKDQD PVAEKIDQEV FYLYATVSQE
710 720 730 740 750
QATELLECDN DKSRIAVLCK DLGVKLMGYD STYDVCSHLI SSISRAQKAR
760
KRLQGPKSLK TGL
Length:763
Mass (Da):83,975
Last modified:July 5, 2004 - 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:iCEA56FBA7D588906
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
A0A0P0XBS5A0A0P0XBS5_ORYSJ
Os08g0143400 protein
Os08g0143400, OSNPB_080143400
691Annotation 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>

<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 BAD13198 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence BAD17024 differs from that shown. Reason: Erroneous gene model prediction.Curated

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
AP004381 Genomic DNA Translation: BAD17023.1
AP004381 Genomic DNA Translation: BAD17024.1 Sequence problems.
AP005542 Genomic DNA Translation: BAD13197.1
AP005542 Genomic DNA Translation: BAD13198.1 Sequence problems.
AP008214 Genomic DNA Translation: BAF22890.1
AP014964 Genomic DNA Translation: BAT03801.1
AK120532 mRNA Translation: BAH00055.1

NCBI Reference Sequences

More...
RefSeqi
XP_015650197.1, XM_015794711.1

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
Os08t0143400-01; Os08t0143400-01; Os08g0143400

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
4344644

Gramene; a comparative resource for plants

More...
Gramenei
Os08t0143400-01; Os08t0143400-01; Os08g0143400

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
osa:4344644

<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
AP004381 Genomic DNA Translation: BAD17023.1
AP004381 Genomic DNA Translation: BAD17024.1 Sequence problems.
AP005542 Genomic DNA Translation: BAD13197.1
AP005542 Genomic DNA Translation: BAD13198.1 Sequence problems.
AP008214 Genomic DNA Translation: BAF22890.1
AP014964 Genomic DNA Translation: BAT03801.1
AK120532 mRNA Translation: BAH00055.1
RefSeqiXP_015650197.1, XM_015794711.1

3D structure databases

SMRiQ6YYZ1
ModBaseiSearch...

Protein-protein interaction databases

STRINGi4530.OS08T0143400-01

Proteomic databases

PaxDbiQ6YYZ1
PRIDEiQ6YYZ1

Genome annotation databases

EnsemblPlantsiOs08t0143400-01; Os08t0143400-01; Os08g0143400
GeneIDi4344644
GrameneiOs08t0143400-01; Os08t0143400-01; Os08g0143400
KEGGiosa:4344644

Phylogenomic databases

eggNOGiKOG0029, Eukaryota
InParanoidiQ6YYZ1
OMAiFFVTRWS
OrthoDBi1034142at2759

Gene expression databases

ExpressionAtlasiQ6YYZ1, baseline and differential
GenevisibleiQ6YYZ1, OS

Family and domain databases

Gene3Di1.10.10.10, 1 hit
3.50.50.60, 1 hit
InterProiView protein in InterPro
IPR002937, Amino_oxidase
IPR036188, FAD/NAD-bd_sf
IPR009057, Homeobox-like_sf
IPR007526, SWIRM
IPR036388, WH-like_DNA-bd_sf
PfamiView protein in Pfam
PF01593, Amino_oxidase, 1 hit
PF04433, SWIRM, 1 hit
SUPFAMiSSF46689, SSF46689, 1 hit
SSF51905, SSF51905, 1 hit
PROSITEiView protein in PROSITE
PS50934, SWIRM, 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 nameiLDL2_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: Q6YYZ1
Secondary accession number(s): B7F607, Q6YYZ0
<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: July 1, 2008
Last sequence update: July 5, 2004
Last modified: December 2, 2020
This is version 101 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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