PDE1B phosphodiesterase 1B [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDE1Bprovided by HGNC
Official Full Name: phosphodiesterase 1Bprovided by HGNC
Primary source: HGNC:HGNC:8775
See related: Ensembl:ENSG00000123360 MIM:171891; AllianceGenome:HGNC:8775
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PDE1B1; PDES1B; HEL-S-79p
Summary: The protein encoded by this gene belongs to the cyclic nucleotide phosphodiesterase (PDE) family, and PDE1 subfamily. Members of the PDE1 family are calmodulin-dependent PDEs that are stimulated by a calcium-calmodulin complex. This PDE has dual-specificity for the second messengers, cAMP and cGMP, with a preference for cGMP as a substrate. cAMP and cGMP function as key regulators of many important physiological processes. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011]
Expression: Broad expression in brain (RPKM 8.5), fat (RPKM 6.8) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.2

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (54549601..54579239)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (54516175..54545790)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (54943385..54973023)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The c.1618G>A, p.Gly540Ser substitution in CNGA3 was identified as the causative mutation for a novel form of ACHM in Awassi sheep. Gene augmentation therapy restored vision in the affected sheep. This novel mutation provides a large-animal model that is valid for most human CNGA3 ACHM patients; the majority of them carry missense rather than premature-termination mutations.
Title: Gene Augmentation Therapy for a Missense Substitution in the cGMP-Binding Domain of Ovine CNGA3 Gene Restores Vision in Day-Blind Sheep.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Selective up-regulation of PDE1B2 upon monocyte-to-macrophage differentiation.
Title: Selective up-regulation of PDE1B2 upon monocyte-to-macrophage differentiation.
PDE1B2 regulates a subset of phenotypic changes that occur upon phorbol-12-myristate-13-acetate-induced differentiation and likely also plays a role in differentiated macrophages by regulating agonist-stimulated cGMP levels
Title: PDE1B2 regulates cGMP and a subset of the phenotypic characteristics acquired upon macrophage differentiation from a monocyte.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat decreases the intracellular levels of cAMP and CREB ser-133 phosphorylation through a signal transduction pathway involving sequential activation of phosphatidylinositol 3-kinase, AKT, and cyclic nucleoside phosphodiesterases	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH78688 (e-PCR)
- UniSTS:48654

RH44485 (e-PCR)
- UniSTS:66073

PDE1B_3295 (e-PCR)
- UniSTS:462390

SHGC-148605 (e-PCR)
- UniSTS:176493

A007D03 (e-PCR)
- UniSTS:80815

MARC_21181-21182:1027091922:1 (e-PCR)
- UniSTS:268504

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3',5'-cyclic-AMP phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed
enables 3',5'-cyclic-AMP phosphodiesterase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables 3',5'-cyclic-GMP phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed
enables calmodulin binding	IEA Inferred from Electronic Annotation more info
enables calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cAMP-mediated signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to granulocyte macrophage colony-stimulating factor stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to macrophage colony-stimulating factor stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in dopamine catabolic process	IEA Inferred from Electronic Annotation more info
involved_in locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in monocyte differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to amphetamine	IEA Inferred from Electronic Annotation more info
involved_in serotonin metabolic process	IEA Inferred from Electronic Annotation more info
involved_in visual learning	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
is_active_in neuronal cell body	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B

Names: 63 kDa Cam-PDE; calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B; calcium/calmodulin-stimulated cyclic nucleotide phosphodiesterase; calmodulin-stimulated phosphodiesterase PDE1B1; cam-PDE 1B; epididymis secretory sperm binding protein Li 79p; phosphodiesterase 1B, calmodulin-dependent; presumed 63kDa form of the type 1 cyclic nucleotide phosphodiesterase family known as PDE1B

NP_000915.1

EC 3.1.4.17

NP_001159447.1

EC 3.1.4.17

NP_001275697.1

EC 3.1.4.17

NP_001275698.1

EC 3.1.4.17

NP_001302463.1

EC 3.1.4.17

NP_001302464.1

EC 3.1.4.17

XP_016874921.1

EC 3.1.4.17

XP_016874922.1

EC 3.1.4.17

XP_047284926.1

EC 3.1.4.17

XP_054228193.1

EC 3.1.4.17

XP_054228194.1

EC 3.1.4.17

XP_054228195.1

EC 3.1.4.17

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.

Genomic

NG_029621.1 RefSeqGene

Range

5209..34847

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000924.4 → NP_000915.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 1

See identical proteins and their annotated locations for NP_000915.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC079310, BC032226, DA254686

Consensus CDS

CCDS8882.1

UniProtKB/Swiss-Prot

Q01064, Q92825, Q96KP3

Related

ENSP00000243052.3, ENST00000243052.8

Conserved Domains (2) summary

pfam00233
Location:222 → 449

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam08499
Location:81 → 137

PDEase_I_N; 3'5'-cyclic nucleotide phosphodiesterase N-terminal
NM_001165975.3 → NP_001159447.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 2

See identical proteins and their annotated locations for NP_001159447.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains a distinct 5' UTR, lacks part of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

BC032226, BP342896, BX538092

Consensus CDS

CCDS53800.1

UniProtKB/Swiss-Prot

Q01064

UniProtKB/TrEMBL

Q7Z364

Related

ENSP00000448519.1, ENST00000550620.1

Conserved Domains (2) summary

pfam00233
Location:202 → 429

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam08499
Location:61 → 117

PDEase_I_N; 3'5'-cyclic nucleotide phosphodiesterase N-terminal
NM_001288768.2 → NP_001275697.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 3

See identical proteins and their annotated locations for NP_001275697.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3 and 5 both encode the same isoform (3).

Source sequence(s)

AK302899, BC032226, BX538092, DA254686

UniProtKB/TrEMBL

Q7Z364

Conserved Domains (1) summary

pfam00233
Location:85 → 312

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
NM_001288769.2 → NP_001275698.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 4

See identical proteins and their annotated locations for NP_001275698.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains a distinct 5' UTR, lacks part of the 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AK296422, BC032226, BX538092

Consensus CDS

CCDS73477.1

UniProtKB/TrEMBL

B4DK72

Related

ENSP00000442559.1, ENST00000538346.5

Conserved Domains (2) summary

pfam00233
Location:181 → 408

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam08499
Location:40 → 96

PDEase_I_N; 3'5'-cyclic nucleotide phosphodiesterase N-terminal
NM_001315534.2 → NP_001302463.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (5) contains a distinct 5' UTR, lacks part of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus compared to isoform 1. Variants 3 and 5 both encode the same isoform (3).

Source sequence(s)

AC068789, BC032226, BX538092

UniProtKB/TrEMBL

Q7Z364

Related

ENST00000394277.7

Conserved Domains (1) summary

pfam00233
Location:85 → 312

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
NM_001315535.2 → NP_001302464.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (6) contains a distinct 5' UTR, lacks part of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (5) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AC068789, AC079310, AK126899, BC032226, BX538092

UniProtKB/TrEMBL

B3KX78

Related

ENST00000542335.5

Conserved Domains (1) summary

pfam00233
Location:18 → 245

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

54549601..54579239

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047428970.1 → XP_047284926.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X1
XM_017019433.2 → XP_016874922.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X3

UniProtKB/TrEMBL

B4DK72

Conserved Domains (2) summary

pfam00233
Location:181 → 408

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam08499
Location:40 → 96

PDEase_I_N; 3'5'-cyclic nucleotide phosphodiesterase N-terminal
XM_017019432.2 → XP_016874921.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

54516175..54545790

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054372218.1 → XP_054228193.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X1
XM_054372220.1 → XP_054228195.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X3

UniProtKB/TrEMBL

B4DK72
XM_054372219.1 → XP_054228194.1 dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X2