ID   ALFL3_ORYSJ             Reviewed;         247 AA.
AC   Q84TV4; A0A0P0W4R7; Q84TC0;
DT   21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2003, sequence version 1.
DT   03-AUG-2022, entry version 122.
DE   RecName: Full=PHD finger protein ALFIN-LIKE 3;
GN   OrderedLocusNames=Os03g0818300, LOC_Os03g60390;
GN   ORFNames=OJ1754_E06.2, OsJ_13123, OSJNBa0094J08.5;
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=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   [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=AAO65855.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC       Sequence=EEE60182.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; AC104433; AAO65855.1; ALT_INIT; Genomic_DNA.
DR   EMBL; AC133007; AAO60037.1; -; Genomic_DNA.
DR   EMBL; DP000009; ABF99565.1; -; Genomic_DNA.
DR   EMBL; AP008209; BAF13621.1; -; Genomic_DNA.
DR   EMBL; AP014959; BAS87067.1; -; Genomic_DNA.
DR   EMBL; CM000140; EEE60182.1; ALT_INIT; Genomic_DNA.
DR   EMBL; AK103363; BAG96042.1; -; mRNA.
DR   RefSeq; XP_015629849.1; XM_015774363.1.
DR   AlphaFoldDB; Q84TV4; -.
DR   SMR; Q84TV4; -.
DR   STRING; 4530.OS03T0818300-01; -.
DR   PaxDb; Q84TV4; -.
DR   PRIDE; Q84TV4; -.
DR   EnsemblPlants; Os03t0818300-01; Os03t0818300-01; Os03g0818300.
DR   GeneID; 4334579; -.
DR   Gramene; Os03t0818300-01; Os03t0818300-01; Os03g0818300.
DR   KEGG; osa:4334579; -.
DR   eggNOG; KOG1632; Eukaryota.
DR   HOGENOM; CLU_058315_1_0_1; -.
DR   InParanoid; Q84TV4; -.
DR   OMA; CGPDREN; -.
DR   OrthoDB; 1370179at2759; -.
DR   Proteomes; UP000000763; Chromosome 3.
DR   Proteomes; UP000007752; Chromosome 3.
DR   Proteomes; UP000059680; Chromosome 3.
DR   Genevisible; Q84TV4; 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..247
FT                   /note="PHD finger protein ALFIN-LIKE 3"
FT                   /id="PRO_0000412941"
FT   ZN_FING         188..240
FT                   /note="PHD-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   REGION          147..178
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        147..177
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   SITE            198
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
FT   SITE            204
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
FT   SITE            208
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
FT   SITE            213
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   247 AA;  27782 MW;  659FFE8CB475504A CRC64;
     MEMAPAAQVA SNPRTVEDIF KDYSARRGAL VRALTSDVDE FFGLCDPDKE NLCLYGLANG
     SWEVALPAEE VPPELPEPAL GINFARDGMN RRDWLSLVAV HSDSWLVSVA FFFAARLNGN
     ERKRLFNMIN DLPTVYEALV DRKHVRDRSG VDSSGKSKHS TKRTGEGQVK RSRVVAEEYE
     DDDEEHNETF CGTCGGLYNA NEFWIGCDIC ERWFHGKCVR ITPAKAEHIK HYKCPDCSSS
     SSKKTRL