Pde6b phosphodiesterase 6B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pde6bprovided by RGD
Official Full Name: phosphodiesterase 6Bprovided by RGD
Primary source: RGD:1311039
See related: EnsemblRapid:ENSRNOG00000000065 AllianceGenome:RGD:1311039
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable 3',5'-cyclic-nucleotide phosphodiesterase activity. Involved in retinal cell apoptotic process. Predicted to be located in photoreceptor outer segment. Predicted to be active in photoreceptor outer segment membrane. Used to study retinitis pigmentosa. Human ortholog(s) of this gene implicated in congenital stationary night blindness autosomal dominant 2 and retinitis pigmentosa 40. Orthologous to human PDE6B (phosphodiesterase 6B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 4.3), Spleen (RPKM 2.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14p22

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (1468302..1511435, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (1323310..1366450, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (2328690..2371913, complement)

Chromosome 14 - NC_086032.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Pde6b knockout rat exhibits photoreceptor degeneration. It may provide a better model for experimental therapy for retinitis pigmentosa because of its slower progression and larger anatomic architecture than the corresponding mouse model.
Title: Development of a Pde6b Gene Knockout Rat Model for Studies of Degenerative Retinal Diseases.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 3',5'-cyclic-AMP phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 3',5'-cyclic-GMP phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cAMP-mediated signaling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within detection of light stimulus	ISO Inferred from Sequence Orthology more info
involved_in entrainment of circadian clock by photoperiod	ISO Inferred from Sequence Orthology more info
involved_in retina development in camera-type eye	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in retinal cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in photoreceptor outer segment	ISO Inferred from Sequence Orthology more info
is_active_in photoreceptor outer segment membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta

Names: phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide; phosphodiesterase 6B, cGMP-specific, rod, beta

NP_001099494.1

EC 3.1.4.35

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_001106024.1 → NP_001099494.1 rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta

See identical proteins and their annotated locations for NP_001099494.1

Status: PROVISIONAL

Source sequence(s)

CH474079

UniProtKB/TrEMBL

A6KPF9, D3ZDI8

Related

ENSRNOP00000000077.5, ENSRNOT00000000077.7

Conserved Domains (2) summary

smart00065
Location:71 → 230

GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases

pfam00233
Location:556 → 801

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase