ALFL8_ORYSJ
ID ALFL8_ORYSJ Reviewed; 254 AA.
AC Q2R837; A0A0P0Y0Z4; Q53M06;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 11-JUL-2006, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=PHD finger protein ALFIN-LIKE 8;
GN OrderedLocusNames=Os11g0244800, LOC_Os11g14010;
GN ORFNames=OsJ_33509, OSJNBa0004P24, OSJNBa0024M06;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG The rice chromosomes 11 and 12 sequencing consortia;
RT "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT genes and recent gene duplications.";
RL BMC Biol. 3:20-20(2005).
RN [2]
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 [3]
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 [4]
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).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
RP GENE FAMILY.
RX PubMed=19154204; DOI=10.1111/j.1365-313x.2009.03795.x;
RA Lee W.Y., Lee D., Chung W.I., Kwon C.S.;
RT "Arabidopsis ING and Alfin1-like protein families localize to the nucleus
RT and bind to H3K4me3/2 via plant homeodomain fingers.";
RL Plant J. 58:511-524(2009).
CC -!- FUNCTION: Histone-binding component that specifically recognizes H3
CC tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription
CC start sites of virtually all active genes. {ECO:0000250}.
CC -!- SUBUNIT: Interacts with H3K4me3 and to a lesser extent with H3K4me2.
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me3.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the Alfin family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAX92933.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAX95841.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC135459; AAX92933.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC138000; AAX95841.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000010; ABA92392.2; -; Genomic_DNA.
DR EMBL; AP008217; BAF27962.1; -; Genomic_DNA.
DR EMBL; AP014967; BAT13403.1; -; Genomic_DNA.
DR EMBL; CM000148; EEE51908.1; -; Genomic_DNA.
DR EMBL; AK103215; BAG95959.1; -; mRNA.
DR RefSeq; XP_015617482.1; XM_015761996.1.
DR AlphaFoldDB; Q2R837; -.
DR SMR; Q2R837; -.
DR STRING; 4530.OS11T0244800-01; -.
DR PaxDb; Q2R837; -.
DR PRIDE; Q2R837; -.
DR EnsemblPlants; Os11t0244800-01; Os11t0244800-01; Os11g0244800.
DR GeneID; 4350183; -.
DR Gramene; Os11t0244800-01; Os11t0244800-01; Os11g0244800.
DR KEGG; osa:4350183; -.
DR eggNOG; KOG1632; Eukaryota.
DR HOGENOM; CLU_058315_1_0_1; -.
DR InParanoid; Q2R837; -.
DR OMA; EHENALC; -.
DR OrthoDB; 1275921at2759; -.
DR Proteomes; UP000000763; Chromosome 11.
DR Proteomes; UP000007752; Chromosome 11.
DR Proteomes; UP000059680; Chromosome 11.
DR Genevisible; Q2R837; OS.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0042393; F:histone binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IBA:GO_Central.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR CDD; cd15613; PHD_AL_plant; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR045104; Alfin.
DR InterPro; IPR021998; Alfin_N.
DR InterPro; IPR044104; PHD_AL_plant.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR12321; PTHR12321; 1.
DR Pfam; PF12165; Alfin; 1.
DR Pfam; PF00628; PHD; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 2: Evidence at transcript level;
KW Chromatin regulator; Metal-binding; Nucleus; Reference proteome;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..254
FT /note="PHD finger protein ALFIN-LIKE 8"
FT /id="PRO_0000412951"
FT ZN_FING 196..248
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 137..194
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 152..166
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 206
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 212
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 216
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 221
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
SQ SEQUENCE 254 AA; 28544 MW; A3C97E781D50BD3A CRC64;
MDGGGAHRTP EDVFRDFRAR RAGMIKALTT DVEKFYQQCD PEKENLCLYG LPNETWEVNL
PAEEVPPELP EPALGINFAR DGMDEKDWLS LVAVHSDTWL LAVAFYFGAR FGFDKESRKR
LFSMINNLPT IYEVVTGTAK KQSKEKTPKT SGKSNKSGTK PSRQPEPNSR GPKMPPPKDE
DDSGGEEEEE EEDHENTLCG ACGDNYGQDE FWICCDACET WFHGKCVKIT PAKAEHIKHY
KCPNCSSSSK RARA
