H33_ORYSJ
ID H33_ORYSJ Reviewed; 136 AA.
AC Q0JCT1; Q71UF0; Q7F8L1; Q8SA80;
DT 24-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 24-JUL-2007, sequence version 2.
DT 03-AUG-2022, entry version 92.
DE RecName: Full=Histone H3.3;
DE AltName: Full=H3.2;
GN Name=H3; Synonyms=RH3, RH3.2A;
GN OrderedLocusNames=Os03g0390600 {ECO:0000312|EMBL:BAS84518.1},
GN LOC_Os03g27310 {ECO:0000305};
GN ORFNames=OSJNBa0017N12.5 {ECO:0000312|EMBL:AAR06361.1};
GN and
GN OrderedLocusNames=Os04g0450800 {ECO:0000312|EMBL:BAF14856.1},
GN LOC_Os04g37780 {ECO:0000305};
GN and
GN OrderedLocusNames=Os06g0130900 {ECO:0000312|EMBL:BAF18607.1},
GN LOC_Os06g04030 {ECO:0000305};
GN ORFNames=P0493C11.10 {ECO:0000312|EMBL:BAA84794.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Ilpoom; TISSUE=Leaf;
RA Lee J.-S.;
RT "Molecular cloning and characterization of histone H3 in rice.";
RL Submitted (SEP-1998) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Xiong A., Yao Q., Peng R., Li X., Fan H.;
RT "Oryza sativa disease-resistent-related protein (RH3) mRNA.";
RL Submitted (JAN-2002) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA], AND INDUCTION.
RC STRAIN=cv. Jiu Caiqing; TISSUE=Leaf;
RX PubMed=16980130; DOI=10.1016/s0379-4172(06)60117-0;
RA Qiu S.-P., Huang J., Pan L.-J., Wang M.-M., Zhang H.-S.;
RT "Salt induces expression of RH3.2A, encoding an H3.2-type histone H3
RT protein in rice (Oryza sativa L.).";
RL Yi Chuan Xue Bao 33:833-840(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [6]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [7]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
CC -!- FUNCTION: Variant histone H3 which replaces conventional H3 in a wide
CC range of nucleosomes in active genes. Constitutes the predominant form
CC of histone H3 in non-dividing cells and is incorporated into chromatin
CC independently of DNA synthesis. Deposited at sites of nucleosomal
CC displacement throughout transcribed genes, suggesting that it
CC represents an epigenetic imprint of transcriptionally active chromatin.
CC Nucleosomes wrap and compact DNA into chromatin, limiting DNA
CC accessibility to the cellular machineries which require DNA as a
CC template. Histones thereby play a central role in transcription
CC regulation, DNA repair, DNA replication and chromosomal stability. DNA
CC accessibility is regulated via a complex set of post-translational
CC modifications of histones, also called histone code, and nucleosome
CC remodeling.
CC -!- SUBUNIT: The nucleosome is a histone octamer containing two molecules
CC each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and
CC two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of
CC DNA.
CC -!- INTERACTION:
CC Q0JCT1; Q6L4L4: SIZ1; NbExp=5; IntAct=EBI-7896995, EBI-7896966;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome {ECO:0000250}.
CC -!- INDUCTION: Up-regulated by salt stress and abscisic acid.
CC {ECO:0000269|PubMed:16980130}.
CC -!- PTM: Acetylation is generally linked to gene activation. Can be
CC acetylated to form H3K9ac, H3K14ac, H3K18ac and H3K23ac. H3K9ac could
CC compete with H3K9me and prevent gene silencing. H3K9ac is restricted to
CC euchromatin (By similarity). {ECO:0000250}.
CC -!- PTM: Methylated to form mainly H3K4me, H3K9me, H3K18me, H3K23me,
CC H3K27me and H3K36me. H3K4me1/2/3, H3K9me3, H3K27me3 and H3K36me1/2/3
CC are typical marks for euchromatin, whereas heterochromatic
CC chromocenters are enriched in H3K9me1/2 and H3K27me1/2. H2BK143ub1 is
CC probably prerequisite for H3K4me (By similarity). {ECO:0000250}.
CC -!- PTM: Can be phosphorylated to form H3S10ph, H3T11ph and H3S28ph.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the histone H3 family. {ECO:0000305}.
CC -!- CAUTION: To ensure consistency between histone entries, we follow the
CC 'Brno' nomenclature for histone modifications, with positions referring
CC to those used in the literature for the 'closest' model organism. Due
CC to slight variations in histone sequences between organisms and to the
CC presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the
CC actual positions of modified amino acids in the sequence generally
CC differ. In this entry the following conventions are used: H3K4me =
CC methylated Lys-5; H3K9ac = acetylated Lys-10; H3K9me = methylated Lys-
CC 10; H3S10ph = phosphorylated Ser-11; H3T11ph = phosphorylated Thr-12;
CC H3K14ac = acetylated Lys-15; H3K18ac = acetylated Lys-19; H3K18me =
CC methylated Lys-19; H3K23ac = acetylated Lys-24; H3K23me = methylated
CC Lys-24; H3K27me = methylated Lys-28; H3S28ph = phosphorylated Ser-29;
CC H3K36me = methylated Lys-37. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF14856.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF093633; AAC78105.1; -; mRNA.
DR EMBL; AF467728; AAL78367.1; -; mRNA.
DR EMBL; AY525328; AAS19511.1; -; mRNA.
DR EMBL; AC092075; AAR06361.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF96358.1; -; Genomic_DNA.
DR EMBL; AP000559; BAA84794.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF12190.1; -; Genomic_DNA.
DR EMBL; AP008210; BAF14856.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008212; BAF18607.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS84518.1; -; Genomic_DNA.
DR EMBL; AP014960; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AP014962; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_015630537.1; XM_015775051.1.
DR RefSeq; XP_015643543.1; XM_015788057.1.
DR AlphaFoldDB; Q0JCT1; -.
DR SMR; Q0JCT1; -.
DR IntAct; Q0JCT1; 1.
DR MINT; Q0JCT1; -.
DR STRING; 4530.OS03T0390600-02; -.
DR PaxDb; Q0JCT1; -.
DR PRIDE; Q0JCT1; -.
DR EnsemblPlants; Os03t0390600-02; Os03t0390600-02; Os03g0390600.
DR GeneID; 4333019; -.
DR GeneID; 4340006; -.
DR Gramene; Os03t0390600-02; Os03t0390600-02; Os03g0390600.
DR KEGG; osa:4333019; -.
DR KEGG; osa:4340006; -.
DR eggNOG; KOG1745; Eukaryota.
DR HOGENOM; CLU_078295_4_0_1; -.
DR InParanoid; Q0JCT1; -.
DR OMA; HIVMART; -.
DR OrthoDB; 1564596at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000000763; Chromosome 4.
DR Proteomes; UP000000763; Chromosome 6.
DR Proteomes; UP000059680; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 4.
DR Proteomes; UP000059680; Chromosome 6.
DR ExpressionAtlas; Q0JCT1; baseline and differential.
DR Genevisible; Q0JCT1; OS.
DR GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046982; F:protein heterodimerization activity; IEA:InterPro.
DR GO; GO:0030527; F:structural constituent of chromatin; IEA:InterPro.
DR Gene3D; 1.10.20.10; -; 1.
DR InterPro; IPR009072; Histone-fold.
DR InterPro; IPR007125; Histone_H2A/H2B/H3.
DR InterPro; IPR000164; Histone_H3/CENP-A.
DR PANTHER; PTHR11426; PTHR11426; 1.
DR Pfam; PF00125; Histone; 1.
DR PRINTS; PR00622; HISTONEH3.
DR SMART; SM00428; H3; 1.
DR SUPFAM; SSF47113; SSF47113; 1.
DR PROSITE; PS00322; HISTONE_H3_1; 1.
DR PROSITE; PS00959; HISTONE_H3_2; 1.
PE 1: Evidence at protein level;
KW Acetylation; Chromosome; DNA-binding; Methylation; Nucleosome core;
KW Nucleus; Phosphoprotein; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250"
FT CHAIN 2..136
FT /note="Histone H3.3"
FT /id="PRO_0000263052"
FT REGION 1..43
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 5
FT /note="N6-methylated lysine"
FT /evidence="ECO:0000250"
FT MOD_RES 10
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 10
FT /note="N6-methylated lysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 11
FT /note="Phosphoserine"
FT /evidence="ECO:0000250"
FT MOD_RES 12
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250"
FT MOD_RES 15
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250"
FT MOD_RES 19
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 19
FT /note="N6-methylated lysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 24
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 24
FT /note="N6-methylated lysine; alternate"
FT /evidence="ECO:0000250"
FT MOD_RES 28
FT /note="N6-methylated lysine"
FT /evidence="ECO:0000250"
FT MOD_RES 29
FT /note="Phosphoserine"
FT /evidence="ECO:0000250"
FT MOD_RES 37
FT /note="N6-methylated lysine; alternate"
FT /evidence="ECO:0000250"
FT CONFLICT 126
FT /note="Q -> K (in Ref. 2; AAL78367)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 136 AA; 15406 MW; 6D72383BF2E9EBE6 CRC64;
MARTKQTARK STGGKAPRKQ LATKAARKSA PTTGGVKKPH RYRPGTVALR EIRKYQKSTE
LLIRKLPFQR LVREIAQDFK TDLRFQSHAV LALQEAAEAY LVGLFEDTNL CAIHAKRVTI
MPKDIQLARR IRGERA
