LOC4332623 phytochrome B-like [Oryza sativa Japonica Group (Japanese rice)] - Gene

Summary

Gene symbol: LOC4332623
Gene description: phytochrome B-like
Locus tag: OSNPB_030309200
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Oryza sativa Japonica Group
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Also known as: PhyB; PHYB1
Expression: Ubiquitous expression in leaves before flowering (RPKM 29.3), flower buds (RPKM 21.6) and 6 other tissues See more
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Genomic context

Location:: chromosome: 3

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_06	current	ASM3414082v1 (GCF_034140825.1)	3	NC_089037.1 (11073435..11081646)
102	previous assembly	IRGSP-1.0 (GCF_001433935.1)	3	NC_029258.1 (11020017..11028186)

Chromosome 3 - NC_089037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Transcriptome profiling of various organs at different developmental stages in rice Transcriptome profiling of various organs at different developmental stages in rice
Description: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds
BioProject: PRJNA243371
Publication: PMID 26387578
Analysis date: Fri Dec 15 20:02:59 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PhyB role in the anther development and pollen viability.
Title: The Rice Phytochrome Genes, PHYA and PHYB, Have Synergistic Effects on Anther Development and Pollen Viability.
OsPhyA influences flowering time mainly by affecting the expression of OsGI under short day and Ghd7 under long day when phytochrome B is absent.
Title: OsPhyA modulates rice flowering time mainly through OsGI under short days and Ghd7 under long days in the absence of phytochrome B.
we showed that OsPIF14 is indeed a phytochrome interacting factor, which preferentially binds to the active form (Pfr) of rice phytochrome B.
Title: Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B.
Phytochrome B Mediates the Regulation of Chlorophyll Biosynthesis through Transcriptional Regulation of ChlH and GUN4 in Rice Seedlings.
Title: Phytochrome B Mediates the Regulation of Chlorophyll Biosynthesis through Transcriptional Regulation of ChlH and GUN4 in Rice Seedlings.

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General gene information

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Gene Ontology Provided by RefSeq

Function	Evidence Code	Pubs
enables phosphorelay sensor kinase activity	IEA Inferred from Electronic Annotation more info	PubMed
enables photoreceptor activity	IEA Inferred from Electronic Annotation more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info	PubMed

Process	Evidence Code	Pubs
involved_in detection of visible light	IEA Inferred from Electronic Annotation more info	PubMed
involved_in protein-tetrapyrrole linkage	IEA Inferred from Electronic Annotation more info	PubMed
involved_in red, far-red light phototransduction	IEA Inferred from Electronic Annotation more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info	PubMed

General protein information

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Preferred Names: phytochrome B

Names: LOC_Os03g19590

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001402143.1 → NP_001389072.1 phytochrome B

Status: VALIDATED

Source sequence(s)

AB109892, AP014959, CI438683

UniProtKB/Swiss-Prot

Q10MG9

UniProtKB/TrEMBL

I3RUD9

RefSeqs of Annotated Genomes: GCF_034140825.1-RS_2024_06

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference ASM3414082v1 Primary Assembly

Genomic

NC_089037.1 Reference ASM3414082v1 Primary Assembly

Range

11073435..11081646

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_015775795.3 → XP_015631281.1 phytochrome B isoform X1

UniProtKB/TrEMBL

I3RUB6, I3RUC2, I3RUC5

Conserved Domains (4) summary

COG0642
Location:863 → 1167

BaeS; Signal transduction histidine kinase [Signal transduction mechanisms]

COG4251
Location:114 → 667

COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]

cd16932
Location:1048 → 1160

HATPase_Phy-like; Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E

pfam00989
Location:663 → 779

PAS; PAS fold