TF1_ORYSJ
ID TF1_ORYSJ Reviewed; 709 AA.
AC Q5ZAY0; Q5ZAX7; Q5ZAX8; Q5ZAX9; Q8LLU2;
DT 29-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Homeobox-leucine zipper protein TF1;
DE AltName: Full=HD-ZIP protein TF1;
DE AltName: Full=Homeodomain transcription factor TF1;
DE AltName: Full=Protein TRANSCRIPTION FACTOR 1;
DE Short=OsTF1;
GN Name=TF1; OrderedLocusNames=Os01g0788800, LOC_Os01g57890;
GN ORFNames=P0415A04.46-1, P0415A04.46-2, P0415A04.46-3, P0415A04.46-4,
GN P0557A01.4-1, P0557A01.4-2, P0557A01.4-3, P0557A01.4-4;
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] (ISOFORM 1), AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Tainung 67; TISSUE=Panicle;
RX PubMed=12091716; DOI=10.1093/pcp/pcf076;
RA Yang J.-Y., Chung M.-C., Tu C.-Y., Leu W.-M.;
RT "OSTF1: a HD-GL2 family homeobox gene is developmentally regulated during
RT early embryogenesis in rice.";
RL Plant Cell Physiol. 43:628-638(2002).
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 MRNA] (ISOFORM 2).
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).
CC -!- FUNCTION: Probable transcription factor. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q5ZAY0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q5ZAY0-2; Sequence=VSP_033317, VSP_033318;
CC -!- DEVELOPMENTAL STAGE: Expressed in the embryo proper and both layers of
CC the integument at 2 days after pollination (DAP). At 3 DAP, strongly
CC expressed in the outer cell layer of the embryo and at lower levels in
CC the integument and the outer endosperm layer (prealeurone layer). From
CC 4 DAP to 6 DAP, expressed in the integument, the scutellar epithelium
CC and embryo axis. Expression stongly decreases from 8 DAP to disappear
CC completely at 10 DAP. Expressed in young seedlings developing roots at
CC the root hair-forming side of epidermal cells.
CC {ECO:0000269|PubMed:12091716}.
CC -!- SIMILARITY: Belongs to the HD-ZIP homeobox family. Class IV subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AK121338; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=BAD53270.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD53271.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD81956.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD81957.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF317882; AAM88945.1; -; mRNA.
DR EMBL; AP003280; BAD81954.1; -; Genomic_DNA.
DR EMBL; AP003280; BAD81955.1; -; Genomic_DNA.
DR EMBL; AP003280; BAD81956.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP003280; BAD81957.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP003345; BAD53268.1; -; Genomic_DNA.
DR EMBL; AP003345; BAD53269.1; -; Genomic_DNA.
DR EMBL; AP003345; BAD53270.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP003345; BAD53271.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008207; BAF06397.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS74713.1; -; Genomic_DNA.
DR EMBL; AK121338; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015632244.1; XM_015776758.1. [Q5ZAY0-1]
DR AlphaFoldDB; Q5ZAY0; -.
DR SMR; Q5ZAY0; -.
DR STRING; 4530.OS01T0788800-01; -.
DR PaxDb; Q5ZAY0; -.
DR PRIDE; Q5ZAY0; -.
DR EnsemblPlants; Os01t0788800-01; Os01t0788800-01; Os01g0788800. [Q5ZAY0-2]
DR GeneID; 4325864; -.
DR Gramene; Os01t0788800-01; Os01t0788800-01; Os01g0788800. [Q5ZAY0-2]
DR KEGG; osa:4325864; -.
DR eggNOG; ENOG502QU3P; Eukaryota.
DR HOGENOM; CLU_015002_2_1_1; -.
DR InParanoid; Q5ZAY0; -.
DR OMA; LMTVEMM; -.
DR OrthoDB; 853265at2759; -.
DR PlantReactome; R-OSA-9631623; Regulation of embryo development.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; Q5ZAY0; OS.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IEA:InterPro.
DR GO; GO:0008289; F:lipid binding; IEA:InterPro.
DR CDD; cd00086; homeodomain; 1.
DR Gene3D; 3.30.530.20; -; 1.
DR InterPro; IPR042160; GLABRA2/ANL2/PDF2/ATML1-like.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017970; Homeobox_CS.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR023393; START-like_dom_sf.
DR InterPro; IPR002913; START_lipid-bd_dom.
DR PANTHER; PTHR45654; PTHR45654; 1.
DR Pfam; PF00046; Homeodomain; 1.
DR Pfam; PF01852; START; 1.
DR SMART; SM00389; HOX; 1.
DR SMART; SM00234; START; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
DR PROSITE; PS50848; START; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Coiled coil; DNA-binding; Homeobox; Nucleus;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..709
FT /note="Homeobox-leucine zipper protein TF1"
FT /id="PRO_0000331748"
FT DOMAIN 212..441
FT /note="START"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00197"
FT DNA_BIND 66..125
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT COILED 166..187
FT /evidence="ECO:0000255"
FT VAR_SEQ 1..80
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_033317"
FT VAR_SEQ 81..83
FT /note="LEG -> MNR (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_033318"
FT CONFLICT 417..418
FT /note="CM -> RV (in Ref. 1; AAM88945)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 709 AA; 78179 MW; E4E9EBCD604BBAE0 CRC64;
MEMNQQHNEG NESFVALMNG FAGDGTATLP NDGEQRMSIP ARELFAAIEA DSGLLPVNSS
NTNEKRKRRL QRLTGKQSEV LEGFFSICGH PDDGQKRHLS ETTGLGLDQV KFWFQNKRTQ
VKTMCWKEEN YKLSVENEIL RDENRRVKIA HCTAVCLTCC NSSVQNQLAV EMERLMGQSE
WLQQEIARSN GTPPAANLAF QLNSSADYVF SGQHDQQMIA ELAKNAMHAL IILAESHVAL
WFPVPGCSYE VLNKMAYDQA YPGDNSANAI GFKTEATRAV SMVMMDYKSV VDFLMDPYNY
RTFFPEVISG AVTNRIYTWP TSDGYNGVIQ LMTVEMMFPS PLVPARKCTF LRYCNVLNEG
LVVVIDVSLD DGSIFSKCRK MPSGFLIQSI RPNSCKVTAI EHVLADDTGV HELYQPCMNG
LVFGARRWVA TMARQSARMR DVHHNKTAPQ VSTKGRKNLM KLADDLLASF AGGIAATGGG
TWTVVIGAGT EKDIRVAYRR TTEGSSSYNA ILSVTASLRL PLPMRKTFDL LRNLTHRCKW
DVLVHGSVVK EEVTIARGVG NDDTVTVLHC KRAGREDRGR TMILQNNGYD ASGSFMVYSQ
IDSELMNTMV LSPSDLPPGR GGPSLYPTGF SLLPDVEAAQ DSSGIALGEV GGTLMTMGFQ
IPVKLASGDR MYSRSAASAI RLMTDTIALV KKTLMNEHSG IYGVSPFHP
