ALFL2_ORYSJ
ID ALFL2_ORYSJ Reviewed; 244 AA.
AC Q8H383; A0A0P0X3Y7; A3BI13; B7EMG8;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=PHD finger protein ALFIN-LIKE 2;
GN OrderedLocusNames=Os07g0233300, LOC_Os07g12910;
GN ORFNames=OsJ_23628, OSJNBa0061L20.107-1;
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=BAG93565.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP005246; BAC21510.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF21155.1; -; Genomic_DNA.
DR EMBL; AP014963; BAT00728.1; -; Genomic_DNA.
DR EMBL; CM000144; EAZ39202.1; -; Genomic_DNA.
DR EMBL; AK073637; BAG93565.1; ALT_INIT; mRNA.
DR RefSeq; XP_015647369.1; XM_015791883.1.
DR AlphaFoldDB; Q8H383; -.
DR SMR; Q8H383; -.
DR STRING; 4530.OS07T0233300-01; -.
DR PaxDb; Q8H383; -.
DR PRIDE; Q8H383; -.
DR EnsemblPlants; Os07t0233300-01; Os07t0233300-01; Os07g0233300.
DR GeneID; 4342784; -.
DR Gramene; Os07t0233300-01; Os07t0233300-01; Os07g0233300.
DR KEGG; osa:4342784; -.
DR eggNOG; KOG1632; Eukaryota.
DR HOGENOM; CLU_058315_1_0_1; -.
DR InParanoid; Q8H383; -.
DR OMA; GMNRIDW; -.
DR OrthoDB; 1370179at2759; -.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000007752; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR ExpressionAtlas; Q8H383; baseline and differential.
DR Genevisible; Q8H383; 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..244
FT /note="PHD finger protein ALFIN-LIKE 2"
FT /id="PRO_0000412939"
FT ZN_FING 187..239
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 137..178
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 137..165
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 197
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 203
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 207
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 212
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT CONFLICT 8..12
FT /note="SPAPR -> FPAPG (in Ref. 4; EAZ39202)"
FT /evidence="ECO:0000305"
FT CONFLICT 56
FT /note="P -> R (in Ref. 5; BAG93565)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 244 AA; 27405 MW; DA9D14887A53F2E0 CRC64;
MEMAAPVSPA PRTVEDIFKD FSGRRAGLVR ALTVDVDEFY GFCDPEKENL CLYGHPNGRW
EVALPAEEVP PELPEPALGI NFARDGMHRR DWLSLVAVHS DSWLLSVAFF FGARLNGNER
KRLFSLINDH PTVLEALSDR KHGRDNKSGA DNGSKSRHSG KRANDVQTKT SRPAVVDDGY
DEEEHSETLC GTCGGRYNAN EFWIGCDICE RWFHGKCVRI TPAKAEHIKH YKCPDCSSSK
KSRQ
