HOX9_ORYSJ
ID HOX9_ORYSJ Reviewed; 840 AA.
AC Q9AV49; F4MGX2; Q6Q7D6; Q6TDS4; Q7XDB2;
DT 29-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Homeobox-leucine zipper protein HOX9;
DE AltName: Full=HD-ZIP protein HOX9;
DE AltName: Full=Homeodomain transcription factor HOX9;
DE AltName: Full=OsHB2;
DE AltName: Full=OsHox9;
GN Name=HOX9; Synonyms=HB2; OrderedLocusNames=Os10g0480200, LOC_Os10g33960;
GN ORFNames=OSJNBa0093B11.11;
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].
RA Yang L., Shen W.-B., Sun Y.-G., Xu L.-L.;
RT "Molecular cloning of Oryza sativa homeodomain leucine-zipper protein Hox9
RT gene as well as the bioinformatics analysis.";
RL Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
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].
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 NUCLEOTIDE SEQUENCE [MRNA] OF 775-840, TISSUE SPECIFICITY, GENE FAMILY, AND
RP NOMENCLATURE.
RC STRAIN=cv. Nipponbare;
RX PubMed=17999151; DOI=10.1007/s11103-007-9255-7;
RA Agalou A., Purwantomo S., Oevernaes E., Johannesson H., Zhu X., Estiati A.,
RA de Kam R.J., Engstroem P., Slamet-Loedin I.H., Zhu Z., Wang M., Xiong L.,
RA Meijer A.H., Ouwerkerk P.B.F.;
RT "A genome-wide survey of HD-Zip genes in rice and analysis of drought-
RT responsive family members.";
RL Plant Mol. Biol. 66:87-103(2008).
RN [8]
RP INDUCTION.
RX PubMed=17804793; DOI=10.1073/pnas.0704339104;
RA Nagasaki H., Itoh J., Hayashi K., Hibara K., Satoh-Nagasawa N., Nosaka M.,
RA Mukouhata M., Ashikari M., Kitano H., Matsuoka M., Nagato Y., Sato Y.;
RT "The small interfering RNA production pathway is required for shoot
RT meristem initiation in rice.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:14867-14871(2007).
CC -!- FUNCTION: Probable transcription factor. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in seedlings, roots, stems, leaf sheaths
CC and blades and panicles. {ECO:0000269|PubMed:17999151}.
CC -!- INDUCTION: Repressed by miR166 in the shoot apicam meristem (SAM)
CC region of devoloping embryo. {ECO:0000269|PubMed:17804793}.
CC -!- SIMILARITY: Belongs to the HD-ZIP homeobox family. Class III subfamily.
CC {ECO:0000305}.
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DR EMBL; AY423716; AAQ98963.1; -; mRNA.
DR EMBL; AC024594; AAK21338.1; -; Genomic_DNA.
DR EMBL; DP000086; AAP54299.1; -; Genomic_DNA.
DR EMBL; DP000086; ABB47795.1; -; Genomic_DNA.
DR EMBL; AP008216; BAF26787.1; -; Genomic_DNA.
DR EMBL; AP014966; BAT11330.1; -; Genomic_DNA.
DR EMBL; AK102603; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AY554037; AAS83424.1; -; mRNA.
DR RefSeq; XP_015614901.1; XM_015759415.1.
DR AlphaFoldDB; Q9AV49; -.
DR SMR; Q9AV49; -.
DR STRING; 4530.OS10T0480200-01; -.
DR PaxDb; Q9AV49; -.
DR PRIDE; Q9AV49; -.
DR EnsemblPlants; Os10t0480200-01; Os10t0480200-01; Os10g0480200.
DR EnsemblPlants; Os10t0480200-02; Os10t0480200-02; Os10g0480200.
DR GeneID; 4348919; -.
DR Gramene; Os10t0480200-01; Os10t0480200-01; Os10g0480200.
DR Gramene; Os10t0480200-02; Os10t0480200-02; Os10g0480200.
DR KEGG; osa:4348919; -.
DR eggNOG; ENOG502QRJM; Eukaryota.
DR HOGENOM; CLU_012517_0_0_1; -.
DR InParanoid; Q9AV49; -.
DR OMA; ITSNHRT; -.
DR OrthoDB; 165228at2759; -.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
DR ExpressionAtlas; Q9AV49; baseline and differential.
DR Genevisible; Q9AV49; OS.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; 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; IPR044830; HD-Zip_III.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR013978; MEKHLA.
DR InterPro; IPR023393; START-like_dom_sf.
DR InterPro; IPR002913; START_lipid-bd_dom.
DR PANTHER; PTHR45950; PTHR45950; 1.
DR Pfam; PF00046; Homeodomain; 1.
DR Pfam; PF08670; MEKHLA; 1.
DR Pfam; PF01852; START; 1.
DR SMART; SM00389; HOX; 1.
DR SMART; SM00234; START; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
DR PROSITE; PS50848; START; 1.
PE 2: Evidence at transcript level;
KW Coiled coil; DNA-binding; Homeobox; Nucleus; Reference proteome;
KW Transcription; Transcription regulation.
FT CHAIN 1..840
FT /note="Homeobox-leucine zipper protein HOX9"
FT /id="PRO_0000331691"
FT DOMAIN 157..385
FT /note="START"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00197"
FT DNA_BIND 26..89
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 135..160
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 86..135
FT /evidence="ECO:0000255"
FT CONFLICT 8
FT /note="R -> P (in Ref. 1; AAQ98963)"
FT /evidence="ECO:0000305"
FT CONFLICT 20
FT /note="Y -> F (in Ref. 1; AAQ98963)"
FT /evidence="ECO:0000305"
FT CONFLICT 151
FT /note="P -> L (in Ref. 1; AAQ98963 and 6; AK102603)"
FT /evidence="ECO:0000305"
FT CONFLICT 319
FT /note="P -> T (in Ref. 1; AAQ98963 and 6; AK102603)"
FT /evidence="ECO:0000305"
FT CONFLICT 436
FT /note="K -> R (in Ref. 1; AAQ98963 and 6; AK102603)"
FT /evidence="ECO:0000305"
FT CONFLICT 584
FT /note="P -> Q (in Ref. 1; AAQ98963 and 6; AK102603)"
FT /evidence="ECO:0000305"
FT CONFLICT 596
FT /note="D -> N (in Ref. 1; AAQ98963 and 6; AK102603)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 840 AA; 92132 MW; 006E521EEDC44767 CRC64;
MAAAVAMRSG SGSDGGGGGY DKAGMDSGKY VRYTPEQVEA LERVYAECPK PSSSRRQQLL
RDCPILANIE PKQIKVWFQN RRCRDKQRKE ASRLQAVNRK LTAMNKLLME ENERLQKQVS
QLVHENAYMK QQLQNPSLGN DTSCESNVTT PQNPLRDASN PSGLLTIAEE TLTEFLSKAT
GTAVDWVPMP GMKPGPDSFG IVAVSHGCRG VAARACGLVN LEPTKIVEIL KDRPSWFRDC
RSLEVFTMFP AGNGGTIELV YMQMYAPTTL VPARDFWTLR YTTTMEDGSL VVCERSLSGS
GGGPSTASAQ QFVRAEMLPS GYLVRPCEGG GSIVHIVDHL DLEAWSVPEV LRPLYESSRV
VAQKMTTAAL RHIRQIAQET SGEVVYALGR QPAVLRTFSQ RLSRGFNDAI SGFNDDGWSV
MGGDGIEDVI IACNAKKVRN TSTSANAFVT PGGVICAKAS MLLQSVPPAV LVRFLREHRS
EWADYNFDAY SASSLKTSSC SLPGLRPMRF SGSQIIMPLA HTVENEEILE VVRLEGQALT
HDDGLMSRDI HLLQLCTGID EKSMGSCFQL VSAPIDELFP DDAPLISSGF RVIPLDMKTD
GTPAGRTLDL ASSLEVGSTA QPTGDASMDD CNLRSVLTIA FQFPYEMHLQ DSVATMARQY
VRSIVSSVQR VSMAISPSRS GLNAGQKIIS GFPEAPTLAR WICQSYQFHL GVELLRQADD
AGEALLKMLW DYEDAILCCS FKEKPVFTFA NEMGLNMLET SLVALQDLSL DKIFDEAGRK
ALYNEIPKLM EQGYVYLPGG VCLSGMGRHV SFEQAVAWKV LGEDNNVHCL AFCFVNWSFV
