ALFL9_ORYSJ
ID ALFL9_ORYSJ Reviewed; 278 AA.
AC Q6YTY3; A0A0P0X8K4; B9FYC5;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=PHD finger protein ALFIN-LIKE 9;
GN OrderedLocusNames=Os07g0608400, LOC_Os07g41740;
GN ORFNames=OsJ_25070, OSJNBa0072I06.37, OSJNBb0018L13.1;
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 [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 [2]
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 [3]
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 [4]
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 [5]
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 [6]
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=EEE67562.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP005895; BAC84634.1; -; Genomic_DNA.
DR EMBL; AP006458; BAD32033.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF22156.1; -; Genomic_DNA.
DR EMBL; AP014963; BAT02587.1; -; Genomic_DNA.
DR EMBL; CM000144; EEE67562.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AK109447; BAG98755.1; -; mRNA.
DR RefSeq; XP_015647114.1; XM_015791628.1.
DR AlphaFoldDB; Q6YTY3; -.
DR SMR; Q6YTY3; -.
DR STRING; 4530.OS07T0608400-01; -.
DR PaxDb; Q6YTY3; -.
DR PRIDE; Q6YTY3; -.
DR EnsemblPlants; Os07t0608400-01; Os07t0608400-01; Os07g0608400.
DR GeneID; 4343868; -.
DR Gramene; Os07t0608400-01; Os07t0608400-01; Os07g0608400.
DR KEGG; osa:4343868; -.
DR eggNOG; KOG1632; Eukaryota.
DR HOGENOM; CLU_058315_1_0_1; -.
DR InParanoid; Q6YTY3; -.
DR OMA; CIKATET; -.
DR OrthoDB; 1275921at2759; -.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000007752; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR Genevisible; Q6YTY3; 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..278
FT /note="PHD finger protein ALFIN-LIKE 9"
FT /id="PRO_0000412953"
FT ZN_FING 209..261
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 138..207
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 259..278
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 141..158
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 219
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 225
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 229
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 234
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
SQ SEQUENCE 278 AA; 30415 MW; ADD18BCC2E50AADA CRC64;
MDAQYNPRTV EEVFRDFKGR RAGLVRALTA DVEDFFRQCD PEKENLCLYG FPNEHWEVNL
PAEEVPPELP EPALGINFAR DGMQEKDWLS MVAVHSDAWL LSVAFYFGAR FGFDKNDRKR
LFGMINDLPT IFEVVSGKSK AKPPSANNHS NSKSKSSNKT KSSEPRAKQP KPQPQPPVKN
EGREEEGGPD DEEGGGGGGG GGREEEHGET LCGACGESYG ADEFWICCDI CEKWFHGKCV
KITPAKAEHI KQYKCPSCSG GNGGGGGVSG NGKRARPS
