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ALFL5_ORYSJ
ID   ALFL5_ORYSJ             Reviewed;         258 AA.
AC   Q60DW3; A0A0P0WMG7;
DT   21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   03-AUG-2022, entry version 116.
DE   RecName: Full=PHD finger protein ALFIN-LIKE 5;
GN   OrderedLocusNames=Os05g0419100, LOC_Os05g34640;
GN   ORFNames=OsJ_18575, P0426G01.9;
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=16261349; DOI=10.1007/s00438-005-0039-y;
RA   Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA   Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA   Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT   "A fine physical map of the rice chromosome 5.";
RL   Mol. Genet. Genomics 274:337-345(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   -!- 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   -!- CAUTION: Lacks the Tyr (here Asp-212), a conserved feature of the
CC       aromatic cage required for the interaction with histone H3K4me3/2.
CC       {ECO:0000305}.
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DR   EMBL; AC137623; AAV25644.1; -; Genomic_DNA.
DR   EMBL; AP008211; BAF17484.1; -; Genomic_DNA.
DR   EMBL; AP014961; BAS94060.1; -; Genomic_DNA.
DR   EMBL; CM000142; EEE63756.1; -; Genomic_DNA.
DR   EMBL; AK121400; BAH00468.1; -; mRNA.
DR   RefSeq; XP_015640195.1; XM_015784709.1.
DR   AlphaFoldDB; Q60DW3; -.
DR   SMR; Q60DW3; -.
DR   STRING; 4530.OS05T0419100-01; -.
DR   PaxDb; Q60DW3; -.
DR   PRIDE; Q60DW3; -.
DR   EnsemblPlants; Os05t0419100-01; Os05t0419100-01; Os05g0419100.
DR   GeneID; 4338816; -.
DR   Gramene; Os05t0419100-01; Os05t0419100-01; Os05g0419100.
DR   KEGG; osa:4338816; -.
DR   eggNOG; KOG1632; Eukaryota.
DR   HOGENOM; CLU_058315_0_0_1; -.
DR   InParanoid; Q60DW3; -.
DR   OMA; TRASKMH; -.
DR   OrthoDB; 1275921at2759; -.
DR   Proteomes; UP000000763; Chromosome 5.
DR   Proteomes; UP000007752; Chromosome 5.
DR   Proteomes; UP000059680; Chromosome 5.
DR   Genevisible; Q60DW3; 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..258
FT                   /note="PHD finger protein ALFIN-LIKE 5"
FT                   /id="PRO_0000412945"
FT   ZN_FING         202..254
FT                   /note="PHD-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   REGION          143..205
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        147..169
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        187..201
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   SITE            218
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
FT   SITE            222
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
FT   SITE            227
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   258 AA;  29105 MW;  FF03F6E17727CF3E CRC64;
     MDGGSGGPYT SRTAEEVFRD FRGRRAGMIK ALTTDVEKFY QLCDPEKENL CLYGYPNETW
     EVTLPAEEVP PEIPEPALGI NFARDGMNEK DWLALVAVHS DSWLLAVAFY FAARFGFDKE
     ARRRLFNMIN NLPTIFEVVT GAAKKQTKEK APNSTNKPNK PSSKMQPRPE SHSKAPKPPA
     PPKDDDESGD EYADEEEEER DNTLCGSCGT NDGKDEFWIC CDSCERWYHG KCVKITPARA
     EHIKHYKCPD CGNKRARA
 
 
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