Reviewed, UniProtKB/Swiss-Prot Q10CQ8 (PHYC_ORYSJ)

Names and origin

Protein names

Recommended name:
    Phytochrome C

Gene names

Name:	PHYC
Ordered Locus Names:	Os03g0752100, LOC_Os03g54084
ORF Names:	OJ1112_G08.5, OSJNBa0032E21.08, OSJNBa0047E24.9, OsJ_012088

Organism

Oryza sativa subsp. japonica (Rice)

Taxonomic identifier

39947 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza

Protein attributes

Sequence length	1137 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at transcript level.

General annotation (Comments)

Function	Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion.
Subunit structure	Homodimer By similarity.
Post-translational modification	Contains one covalently linked phytochromobilin chromophore By similarity.
Sequence similarities	Belongs to the phytochrome family. Contains 1 GAF domain. Contains 1 histidine kinase domain. Contains 1 PAC (PAS-associated C-terminal) domain. Contains 2 PAS (PER-ARNT-SIM) domains.
Sequence caution	The sequence ABF98917.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Sensory transduction Transcription Transcription regulation
Domain	Repeat
Ligand	Chromophore
Molecular function	Photoreceptor protein Receptor
Gene Ontology (GO)
Biological process	peptidyl-histidine phosphorylation Inferred from electronic annotation. Source: InterPro protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW protein-tetrapyrrole linkage Inferred from electronic annotation. Source: InterPro red, far-red light phototransduction Inferred from electronic annotation. Source: InterPro regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW signal transduction Inferred from electronic annotation. Source: InterPro transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	membrane Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: InterPro G-protein coupled photoreceptor activity Inferred from electronic annotation. Source: InterPro protein homodimerization activity Inferred from electronic annotation. Source: InterPro two-component sensor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1137	1137	Phytochrome C		PRO_0000171979
Regions
	Domain	217 – 400	184	GAF
	Domain	620 – 690	71	PAS 1
	Domain	750 – 824	75	PAS 2
	Domain	904 – 1124	221	Histidine kinase
Sites
	Binding site	322	1	Phytochromobilin chromophore (covalent; via 1 link) By similarity
Experimental info
	Sequence conflict	279	1	F → S in AAB41996. Ref.6
	Sequence conflict	292	1	C → S in AAB41996. Ref.6

Sequences

	Sequence		Length	Mass (Da)
	Q10CQ8-1 [UniParc]. Last modified August 22, 2006. Version 1. Checksum: F2A520181CFE7B32	FASTA	1,137	125,983
	10 20 30 40 50 60 MSSSRSNNRA TCSRSSSARS KHSARVVAQT PMDAQLHAEF EGSQRHFDYS SSVGAANRSG 70 80 90 100 110 120 ATTSNVSAYL QNMQRGRFVQ PFGCLLAVHP ETFALLAYSE NAAEMLDLTP HAVPTIDQRE 130 140 150 160 170 180 ALAVGTDVRT LFRSHSFVAL QKAATFGDVN LLNPILVHAR TSGKPFYAIM HRIDVGLVID 190 200 210 220 230 240 LEPVNPVDLP VTATGAIKSY KLAARAIARL QSLPSGNLSL LCDVLVREVS ELTGYDRVMA 250 260 270 280 290 300 YKFHEDEHGE VIAECKRSDL EPYLGLHYPA TDIPQASRFL FMKNKVRMIC DCSATPVKII 310 320 330 340 350 360 QDDSLTQPIS ICGSTLRAPH GCHAQYMASM GSVASLVMSV TINEDEDDDG DTGSDQQPKG 370 380 390 400 410 420 RKLWGLMVCH HTSPRFVPFP LRYACEFLLQ VFGIQINKEV ELAAQAKERH ILRTQTLLCD 430 440 450 460 470 480 MLLRDAPVGI FTQSPNVMDL VKCDGAALYY QNQLWVLGST PSEAEIKNIV AWLQEYHDGS 490 500 510 520 530 540 TGLSTDSLVE AGYPGAAALG DVVCGMAAIK ISSKDFIFWF RSHTAKEIKW GGAKHEPIDA 550 560 570 580 590 600 DDNGRKMHPR SSFKAFLEVV KWRSVPWEDV EMDAIHSLQL ILRGSLQDED ANKNNNAKSI 610 620 630 640 650 660 VTAPSDDMKK IQGLLELRTV TNEMVRLIET ATAPILAVDI TGSINGWNNK AAELTGLPVM 670 680 690 700 710 720 EAIGKPLVDL VIDDSVEVVK QILNSALQGI EEQNLQIKLK TFNHQENNGP VILMVNACCS 730 740 750 760 770 780 RDLSEKVVGV CFVAQDMTGQ NIIMDKYTRI QGDYVAIVKN PSELIPPIFM INDLGSCLEW 790 800 810 820 830 840 NEAMQKITGI KREDAVDKLL IGEVFTHHEY GCRVKDHGTL TKLSILMNTV ISGQDPEKLL 850 860 870 880 890 900 FGFFNTDGKY IESLMTATKR TDAEGKITGA LCFLHVASPE LQHALQVQKM SEQAAMNSFK 910 920 930 940 950 960 ELTYIRQELR NPLNGMQFTR NLLEPSDLTE EQRKLLASNV LCQEQLKKIL HDTDLESIEQ 970 980 990 1000 1010 1020 CYTEMSTVDF NLEEALNTVL MQAMPQSKEK QISIDRDWPA EVSCMHLCGD NLRLQQVLAD 1030 1040 1050 1060 1070 1080 FLACMLQFTQ PAEGPIVLQV IPRMENIGSG MQIAHLEFRL VHPAPGVPEA LIQEMFRHSP 1090 1100 1110 1120 1130 GASREGLGLY ISQKLVKTMS GTVQYLRESE SSSFIVLVEF PVAQLSTKRC KASTSKF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Phytochrome C (PHYC) gene in rice: isolation and characterization of a complete coding sequence." Tahir M., Kanegae H., Takano M. Plant Gene Register PGR98-210 Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Nipponbare.
[2]	"Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species." The rice chromosome 3 sequencing consortium Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B., Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T., Fadrosh D., Bera J., Weaver B., Jin S. , Johri S., Reardon M., Webb K., Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T., Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R., Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J., Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S., Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M., Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M., Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L., O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R., Jin W., Lee H.R., Jiang J., Jackson S. Genome Res. 15:1284-1291(2005) [PubMed: 16109971] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[3]	"The map-based sequence of the rice genome." International rice genome sequencing project (IRGSP) Nature 436:793-800(2005) [PubMed: 16100779] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[4]	"Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana." The rice annotation project (RAP) Genome Res. 17:175-183(2007) [PubMed: 17210932] [Abstract] Cited for: GENOME REANNOTATION. Strain: cv. Nipponbare.
[5]	"The genomes of Oryza sativa: a history of duplications." Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L. , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H. PLoS Biol. 3:266-281(2005) [PubMed: 15685292] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[6]	"The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms." Mathews S., Sharrock R.A. Mol. Biol. Evol. 13:1141-1150(1996) [PubMed: 8865668] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 275-378.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AB018442 mRNA. Translation: BAA74448.1. AC092556 Genomic DNA. Translation: AAR87239.1. AC135225 Genomic DNA. Translation: AAP68360.1. AF377947 Genomic DNA. Translation: AAM34402.1. DP000009 Genomic DNA. Translation: ABF98915.1. DP000009 Genomic DNA. Translation: ABF98917.1. Sequence problems. AP008209 Genomic DNA. Translation: BAF13210.1. CM000140 Genomic DNA. Translation: EAZ28605.1. U61207 Genomic DNA. Translation: AAB41996.1.
PIR	T04149.
RefSeq	NP_001051296.1.
UniGene	Os.3383
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	4334135.
KEGG	osa:4334135.
Organism-specific databases
Gramene	Q9ZWI9.
Family and domain databases
InterPro	IPR003594. ATP_bd_ATPase. IPR003018. GAF. IPR001610. PAC. IPR000014. PAS. IPR013654. PAS_2. IPR013767. PAS_fold. IPR016132. Phyto_chromo_attachment. IPR013516. Phyto_chromo_BS. IPR001294. Phytochrome. IPR012129. Phytochrome_A-E. IPR013515. Phytochrome_Cr. IPR003661. Sig_transdc_His_kin_sub1_dim/P. IPR005467. Sig_transdc_His_kinase_core. [Graphical view]
Gene3D	G3DSA:3.30.565.10. ATP_bd_ATPase. 1 hit.
Pfam	PF01590. GAF. 1 hit. PF02518. HATPase_c. 1 hit. PF00512. HisKA. 1 hit. PF00989. PAS. 2 hits. PF08446. PAS_2. 1 hit. PF00360. Phytochrome. 1 hit. [Graphical view]
PIRSF	PIRSF000084. Phytochrome. 1 hit.
PRINTS	PR01033. PHYTOCHROME.
SMART	SM00065. GAF. 1 hit. SM00387. HATPase_c. 1 hit. SM00388. HisKA. 1 hit. SM00086. PAC. 1 hit. SM00091. PAS. 2 hits. [Graphical view]
TIGRFAMs	TIGR00229. sensory_box. 1 hit.
PROSITE	PS50109. HIS_KIN. 1 hit. PS50112. PAS. 2 hits. PS00245. PHYTOCHROME_1. 1 hit. PS50046. PHYTOCHROME_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PHYC_ORYSJ

Accession

Primary (citable) accession number: Q10CQ8
Secondary accession number(s): P93429 , Q10CQ9, Q7FUM6, Q9M7A9, Q9ZWI9

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	August 22, 2006
Last modified:	July 7, 2009
This is version 26 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)