ALFL6_ARATH
ID ALFL6_ARATH Reviewed; 256 AA.
AC Q8S8M9; F4IQE0; Q8LAH0;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 25-MAY-2022, entry version 127.
DE RecName: Full=PHD finger protein ALFIN-LIKE 6;
DE Short=Protein AL6;
GN Name=AL6; OrderedLocusNames=At2g02470; ORFNames=T16F16.26;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP GENE FAMILY, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
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 -!- INTERACTION:
CC Q8S8M9-2; Q8GXR6: At3g58630/F14P22_220; NbExp=3; IntAct=EBI-15223069, EBI-4457957;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19154204}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8S8M9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8S8M9-2; Sequence=VSP_041817;
CC -!- TISSUE SPECIFICITY: Ubiquitously expressed.
CC {ECO:0000269|PubMed:19154204}.
CC -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me3.
CC {ECO:0000250}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the Alfin family. {ECO:0000305}.
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DR EMBL; AC005312; AAM15031.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05583.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05584.1; -; Genomic_DNA.
DR EMBL; BT003905; AAO41953.1; -; mRNA.
DR EMBL; BT005004; AAO50537.1; -; mRNA.
DR EMBL; AY087820; AAM65374.1; -; mRNA.
DR PIR; A84437; A84437.
DR PIR; T00616; T00616.
DR RefSeq; NP_001189502.1; NM_001202573.2. [Q8S8M9-2]
DR RefSeq; NP_178351.1; NM_126302.3. [Q8S8M9-1]
DR AlphaFoldDB; Q8S8M9; -.
DR SMR; Q8S8M9; -.
DR BioGRID; 179; 12.
DR IntAct; Q8S8M9; 3.
DR STRING; 3702.AT2G02470.1; -.
DR iPTMnet; Q8S8M9; -.
DR PaxDb; Q8S8M9; -.
DR PRIDE; Q8S8M9; -.
DR ProteomicsDB; 245068; -. [Q8S8M9-1]
DR EnsemblPlants; AT2G02470.1; AT2G02470.1; AT2G02470. [Q8S8M9-1]
DR EnsemblPlants; AT2G02470.2; AT2G02470.2; AT2G02470. [Q8S8M9-2]
DR GeneID; 814776; -.
DR Gramene; AT2G02470.1; AT2G02470.1; AT2G02470. [Q8S8M9-1]
DR Gramene; AT2G02470.2; AT2G02470.2; AT2G02470. [Q8S8M9-2]
DR KEGG; ath:AT2G02470; -.
DR Araport; AT2G02470; -.
DR TAIR; locus:2056281; AT2G02470.
DR eggNOG; KOG1632; Eukaryota.
DR InParanoid; Q8S8M9; -.
DR OMA; PSKMVKM; -.
DR PhylomeDB; Q8S8M9; -.
DR PRO; PR:Q8S8M9; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q8S8M9; baseline and differential.
DR Genevisible; Q8S8M9; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
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; IPI:TAIR.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0016036; P:cellular response to phosphate starvation; IMP:TAIR.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0055065; P:metal ion homeostasis; IMP:TAIR.
DR GO; GO:0048767; P:root hair elongation; IMP:TAIR.
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 1: Evidence at protein level;
KW Alternative splicing; Chromatin regulator; Metal-binding; Nucleus;
KW Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..256
FT /note="PHD finger protein ALFIN-LIKE 6"
FT /id="PRO_0000412933"
FT ZN_FING 200..252
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 144..200
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 144..173
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 182..199
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 210
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 216
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 220
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 225
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT VAR_SEQ 162..170
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_041817"
FT CONFLICT 170
FT /note="S -> T (in Ref. 4; AAM65374)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 256 AA; 28847 MW; 9A033A5355BE4953 CRC64;
MEGITHPIPR TVEEVFSDFR GRRAGLIKAL TNDMVKFYQT CDPEKENLCL YGLPNETWEV
NLPVEEVPPE LPEPALGINF ARDGMQEKDW VSLVAVHSDS WLLSVAFYFG ARFGFGKNER
KRLFQMINEL PTIFEVVSGN AKQSKDLSVN NNNSKSKPSG VKSRQSESLS KVAKMSSPPP
KEEEEEEDES EDESEDDEQG AVCGACGDNY GTDEFWICCD ACEKWFHGKC VKITPAKAEH
IKHYKCPTCS NKRARP
