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ALFL6_ORYSJ
ID   ALFL6_ORYSJ             Reviewed;         272 AA.
AC   Q7F2Z1; A0A0P0VBC6; O49228;
DT   21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT   15-FEB-2005, sequence version 1.
DT   03-AUG-2022, entry version 114.
DE   RecName: Full=PHD finger protein ALFIN-LIKE 6;
GN   OrderedLocusNames=Os01g0887700, LOC_Os01g66420;
GN   ORFNames=B1099D03.10, OsJ_04343, P0434C04.30;
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. Ilpoombyeo; TISSUE=Seedling;
RA   Yoon U.H., Hahn J.H., Yun C.-H., Eun M.Y.;
RT   "The rice genome contains at least two different genes encoding nucleic
RT   acid binding proteins.";
RL   Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12447438; DOI=10.1038/nature01184;
RA   Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA   Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA   Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA   Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA   Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA   Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA   Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA   Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA   Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA   Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA   Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA   Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA   Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT   "The genome sequence and structure of rice chromosome 1.";
RL   Nature 420:312-316(2002).
RN   [3]
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   [4]
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   [5]
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   [6]
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   [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-226), 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; AF047428; AAC98969.1; -; mRNA.
DR   EMBL; AP003346; BAD82135.1; -; Genomic_DNA.
DR   EMBL; AP003431; BAB92630.1; -; Genomic_DNA.
DR   EMBL; AP008207; BAF06950.1; -; Genomic_DNA.
DR   EMBL; AP014957; BAS75622.1; -; Genomic_DNA.
DR   EMBL; CM000138; EAZ14421.1; -; Genomic_DNA.
DR   PIR; T02745; T02745.
DR   RefSeq; XP_015621936.1; XM_015766450.1.
DR   AlphaFoldDB; Q7F2Z1; -.
DR   SMR; Q7F2Z1; -.
DR   STRING; 4530.OS01T0887700-01; -.
DR   PaxDb; Q7F2Z1; -.
DR   PRIDE; Q7F2Z1; -.
DR   EnsemblPlants; Os01t0887700-01; Os01t0887700-01; Os01g0887700.
DR   GeneID; 4324896; -.
DR   Gramene; Os01t0887700-01; Os01t0887700-01; Os01g0887700.
DR   KEGG; osa:4324896; -.
DR   eggNOG; KOG1632; Eukaryota.
DR   HOGENOM; CLU_058315_0_0_1; -.
DR   InParanoid; Q7F2Z1; -.
DR   OMA; MSGAMRT; -.
DR   OrthoDB; 1275921at2759; -.
DR   Proteomes; UP000000763; Chromosome 1.
DR   Proteomes; UP000007752; Chromosome 1.
DR   Proteomes; UP000059680; Chromosome 1.
DR   ExpressionAtlas; Q7F2Z1; baseline and differential.
DR   Genevisible; Q7F2Z1; 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..272
FT                   /note="PHD finger protein ALFIN-LIKE 6"
FT                   /id="PRO_0000412947"
FT   ZN_FING         216..268
FT                   /note="PHD-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   REGION          1..24
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          162..218
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        163..182
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        183..200
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        201..215
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   SITE            232
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
FT   SITE            236
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
FT   SITE            241
FT                   /note="Histone H3K4me3 binding"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   272 AA;  29604 MW;  964FDFC13AFFC7E2 CRC64;
     MEGGGGGGGG GGGGGGGGGG GGAPYATRTA EEVFRDLRGR RAGMIKALTT DVEKFYKLCD
     PEKENLCLYG YPNETWEVTL PAEEVPPEIP EPALGINFAR DGMNEKDWLA LVAVHSDSWL
     LSVAFYFGAR FGFDREARRR LFNMINNLPT IFEVVTGAAK KQAKEKTPNS SSKSNKPSSK
     VQSKAESRSK SKLSAPKDEE GSGDDEGEEE EDDHDNTLCG TCGTNDGKDE FWICCDNCEK
     WYHGKCVKIT PARAEHIKQY KCPDCTNKRA RA
 
 
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