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Entry version 81 (12 Aug 2020)
Sequence version 2 (11 Sep 2007)
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Protein

Phytochrome C

Gene

PHYC

Organism
Oryza sativa subsp. indica (Rice)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Protein inferred from homologyi <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei322Phytochromobilin chromophore (covalent; via 1 link)By similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionPhotoreceptor protein, Receptor
Biological processSensory transduction, Transcription, Transcription regulation
LigandChromophore

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Phytochrome C
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:PHYC
ORF Names:OsI_013116
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiOryza sativa subsp. indica (Rice)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri39946 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000007015 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 3

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003008611 – 1137Phytochrome CAdd BLAST1137

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Contains one covalently linked phytochromobilin chromophore.By similarity

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
A2XM23

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

By similarity

GO - Molecular functioni

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
A2XM23

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini217 – 400GAFAdd BLAST184
Domaini620 – 690PAS 1PROSITE-ProRule annotationAdd BLAST71
Domaini750 – 824PAS 2PROSITE-ProRule annotationAdd BLAST75
Domaini904 – 1124Histidine kinasePROSITE-ProRule annotationAdd BLAST221

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the phytochrome family.Curated

Keywords - Domaini

Repeat

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00082, HisKA, 1 hit
cd00130, PAS, 2 hits

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.450.270, 1 hit
3.30.450.40, 1 hit
3.30.565.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003018, GAF
IPR029016, GAF-like_dom_sf
IPR003594, HATPase_C
IPR036890, HATPase_C_sf
IPR005467, His_kinase_dom
IPR003661, HisK_dim/P
IPR000014, PAS
IPR035965, PAS-like_dom_sf
IPR013654, PAS_2
IPR013767, PAS_fold
IPR016132, Phyto_chromo_attachment
IPR013516, Phyto_chromo_BS
IPR001294, Phytochrome
IPR012129, Phytochrome_A-E
IPR013515, Phytochrome_cen-reg
IPR043150, Phytochrome_PHY

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01590, GAF, 1 hit
PF02518, HATPase_c, 1 hit
PF00512, HisKA, 1 hit
PF00989, PAS, 2 hits
PF08446, PAS_2, 1 hit
PF00360, PHY, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF000084, Phytochrome, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR01033, PHYTOCHROME

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00065, GAF, 1 hit
SM00387, HATPase_c, 1 hit
SM00388, HisKA, 1 hit
SM00091, PAS, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF55785, SSF55785, 3 hits
SSF55874, SSF55874, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00229, sensory_box, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50109, HIS_KIN, 1 hit
PS50112, PAS, 2 hits
PS00245, PHYTOCHROME_1, 1 hit
PS50046, PHYTOCHROME_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

A2XM23-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSSSRSNNRA TCSRSSSARS KHSARVVAQT PMDAQLHAEF EGSQRHFDYS
60 70 80 90 100
SSVGAANRSG ATTSNVSAYL QNMQRGRFVQ PFGCLLAVHP ETFALLAYSE
110 120 130 140 150
NAAEMLDLTP HAVPTIDQRE ALAVGTDVRT LFRSHSFVAL QKAATFGDVN
160 170 180 190 200
LLNPILVHAR TSGKPFYAIM HRIDVGLVID LEPVNPVDLP VTATGAIKSY
210 220 230 240 250
KLAARAIARL QSLPSGNLSL LCDVLVREVS ELTGYDRVMA YKFHEDEHGE
260 270 280 290 300
VIAECKRSDL EPYLGLHYPA TDIPQASRFL FMKNKVRMIC DCSATPVKII
310 320 330 340 350
QDDSLTQPIS ICGSTLRAPH GCHAQYMASM GSVASLVMSV TINEDEDDDG
360 370 380 390 400
DTGSDQQPKG RKLWGLMVCH HTSPRFVPFP LRYACEFLLQ VFGIQINKEV
410 420 430 440 450
ELAAQAKERH ILRTQTLLCD MLLRDAPVGI FTQSPNVMDL VKCDGAALYY
460 470 480 490 500
QNQLWVLGST PSEAEIKNIV AWLQEYHDGS TGLSTDSLVE AGYPGAAALG
510 520 530 540 550
DVVYGMAAIK ISSKDFIFWF RSHTAKEIKW GGAKHEPIDA DDNGRKMHPR
560 570 580 590 600
SSFKAFLEVV KWRSVPWEDV EMDAIHSLQL ILRGSLQDED ANKNNNAKSI
610 620 630 640 650
VTAPSDDMKK IQGLLELRTV TNEMVRLIET ATAPILAVDI TGSINGWNNK
660 670 680 690 700
AAELTGLPVM EAIGKPLVDL VIDDSVEVVK QILNSALQGI EEQNLQIKLK
710 720 730 740 750
TFNHQENNGP VILMVNACCS RDLSEKVVGV CFVAQDMTGQ NIIMDKYTRI
760 770 780 790 800
QGDYVAIVKN PSELIPPIFM INDLGSCLEW NEAMQKITGI KREDAVDKLL
810 820 830 840 850
IGEVFTHHEY GCRVKDHGTL TKLSILMNTV ISGQDPEKLL FGFFNTDGKY
860 870 880 890 900
IESLMTATKR TDAEGKITGA LCFLHVASPE LQHALQVQKM SEQAAMNSFK
910 920 930 940 950
ELTYIRQELR NPLNGMQFTR NLLEPSDLTE EQRKLLASNV LCQEQLKKIL
960 970 980 990 1000
HDTDLESIEQ CYTEMSTVDF NLEEALNTVL MQAMPQSKEK QISIDRDWPA
1010 1020 1030 1040 1050
EVSCMHLCGD NLRLQQVLAD FLACMLQFTQ PAEGPIVLQV IPRMENIGSG
1060 1070 1080 1090 1100
MQIAHLEFRL VHPAPGVPEA LIQEMFRHSP GASREGLGLY ISQKLVKTMS
1110 1120 1130
GTVQYLRESE SSSFIVLVEF PVAQLSTKRC KASTSKF
Length:1,137
Mass (Da):126,043
Last modified:September 11, 2007 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i3E56573767247B36
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence EAY91883 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti504Y → C in AAF66603 (PubMed:11094977).Curated1
Sequence conflicti1025M → T in AAF66603 (PubMed:11094977).Curated1
Sequence conflicti1109S → A in AAF66603 (PubMed:11094977).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AF141942 Genomic DNA Translation: AAF66603.1
CM000128 Genomic DNA Translation: EAY91883.1 Sequence problems.

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF141942 Genomic DNA Translation: AAF66603.1
CM000128 Genomic DNA Translation: EAY91883.1 Sequence problems.

3D structure databases

SMRiA2XM23
ModBaseiSearch...

Proteomic databases

PRIDEiA2XM23

Family and domain databases

CDDicd00082, HisKA, 1 hit
cd00130, PAS, 2 hits
Gene3Di3.30.450.270, 1 hit
3.30.450.40, 1 hit
3.30.565.10, 1 hit
InterProiView protein in InterPro
IPR003018, GAF
IPR029016, GAF-like_dom_sf
IPR003594, HATPase_C
IPR036890, HATPase_C_sf
IPR005467, His_kinase_dom
IPR003661, HisK_dim/P
IPR000014, PAS
IPR035965, PAS-like_dom_sf
IPR013654, PAS_2
IPR013767, PAS_fold
IPR016132, Phyto_chromo_attachment
IPR013516, Phyto_chromo_BS
IPR001294, Phytochrome
IPR012129, Phytochrome_A-E
IPR013515, Phytochrome_cen-reg
IPR043150, Phytochrome_PHY
PfamiView protein in Pfam
PF01590, GAF, 1 hit
PF02518, HATPase_c, 1 hit
PF00512, HisKA, 1 hit
PF00989, PAS, 2 hits
PF08446, PAS_2, 1 hit
PF00360, PHY, 1 hit
PIRSFiPIRSF000084, Phytochrome, 1 hit
PRINTSiPR01033, PHYTOCHROME
SMARTiView protein in SMART
SM00065, GAF, 1 hit
SM00387, HATPase_c, 1 hit
SM00388, HisKA, 1 hit
SM00091, PAS, 2 hits
SUPFAMiSSF55785, SSF55785, 3 hits
SSF55874, SSF55874, 1 hit
TIGRFAMsiTIGR00229, sensory_box, 1 hit
PROSITEiView protein in PROSITE
PS50109, HIS_KIN, 1 hit
PS50112, PAS, 2 hits
PS00245, PHYTOCHROME_1, 1 hit
PS50046, PHYTOCHROME_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPHYC_ORYSI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: A2XM23
Secondary accession number(s): P93429
, Q7FUM6, Q9M7A9, Q9ZWI9
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: September 11, 2007
Last modified: August 12, 2020
This is version 81 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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