FlyBase Gene Report: Dmel\Pp1-Y1

General Information

Symbol

Dmel\Pp1-Y1

Species

D. melanogaster

Name

Protein phosphatase 1, Y-linked 1

Annotation Symbol

CG41534

Feature Type

protein_coding_gene

FlyBase ID

FBgn0261399

Gene Model Status

Current

Stock Availability

4 publicly available

Enzyme Name (EC)

protein-serine/threonine phosphatase (3.1.3.16)

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

Sequence location

Y:9,833..10,786 [+]

Recombination map

Y-

RefSeq locus

NC_024512 REGION:9833..10786

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

NCBI

UCSC

Ensembl

Function

Gene Ontology (GO) Annotations (4 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables hydrolase activity

inferred from electronic annotation with InterPro:IPR004843, InterPro:IPR006186

(InterPro Project Members, 2004-)

enables protein serine/threonine phosphatase activity

inferred from biological aspect of ancestor with PANTHER:PTN000185233

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with MGI:MGI:104871

(Gene Ontology Curators, 2002-)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000185233

(GO Reference Genome Project, 2011-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000185231

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

PPP FAMILY PROTEIN SERINE/THREONINE PHOSPHATASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

protein serine/threonine phosphatase activity

(1) H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate (3.1.3.16)

(2) H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate (3.1.3.16)

Summaries

Gene Group (FlyBase)

PPP FAMILY PROTEIN SERINE/THREONINE PHOSPHATASES -: The Phosphoprotein Phosphatase (PPP) family members are serine/threonine phosphatases. They often function in association with regulatory subunits. (Adapted from PMID:11230548 and PMID:19879837).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Pp1-Y1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry A8QI94)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 6.01

Sequence Ontology: Class of Gene

gene

nuclear_gene

(Drosophila Heterochromatin Genome Project, 2007)

protein_coding_gene

(Drosophila Heterochromatin Genome Project, 2007)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Pp1-Y1-RC

FBtr0346674

NM_001110682

954

317

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Pp1-Y1-PC

FBpp0312287

36.8

317

7.73

A8QI94

NP_001104152

EDP27872

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Pp1-Y1 using the Feature Mapper tool.

External Data

Crossreferences

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

NA

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

testis

(Adám et al., 2010)

cyst cell of testis

(Adám et al., 2010)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

P-stage

organism

(Adám et al., 2010)

adult stage | male

organism

(Adám et al., 2010)

Additional Descriptive Data

Pp1-Y1 transcript is detected in pupae and in male adult, but not in embryos, larvae, or adult female adults. In situ analysis of male adults shows that expression of PpD1-Y1 transcript is testis-specific.

(Adám et al., 2010)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Pp1-Y1 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Pp1-Y1

View exonic expression by tissue for Dmel\Pp1-Y1

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

5740113/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0261399

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0261399

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Pp1-Y1

Transgenic constructs containing regulatory region of Pp1-Y1

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (15)

Hsap\PPP1CA

6 of 14

Yes

Hsap\PPP1CC

6 of 14

Yes

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (14)

Rnor\Ppp1ca

6 of 14

Yes

Rnor\Ppp1cc

6 of 14

Yes

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

1 of 14

Mus musculus (laboratory mouse) (14)

Mmus\Ppp1ca

6 of 14

Yes

5 of 14

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (15)

Xtro\ppp1cc

6 of 13

Yes

4 of 13

3 of 13

3 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (18)

Drer\ppp1caa

6 of 14

Yes

Drer\ppp1cab

6 of 14

Yes

Drer\ppp1cc

6 of 14

Yes

4 of 14

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (47)

Cele\gsp-2

7 of 14

Yes

5 of 14

5 of 14

5 of 14

5 of 14

5 of 14

5 of 14

5 of 14

5 of 14

5 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (9)

Agam\AgaP_AGAP011166

5 of 12

Yes

4 of 12

4 of 12

4 of 12

3 of 12

2 of 12

2 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (29)

Atha\TOPP3

6 of 13

Yes

Atha\TOPP7

6 of 13

Yes

5 of 13

5 of 13

5 of 13

5 of 13

4 of 13

4 of 13

4 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (12)

Scer\GLC7

5 of 13

Yes

4 of 13

4 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (10)

Spom\dis2

5 of 12

Yes

4 of 12

3 of 12

3 of 12

3 of 12

2 of 12

2 of 12

2 of 12

2 of 12

1 of 12

Escherichia coli (enterobacterium) (2)

Ecol\pphA

1 of 11

Yes

Ecol\pphB

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Pp1-Y1. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (19)

flw

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

mts

4 of 13

Pp4-19C

4 of 13

CG11597

3 of 13

PpV

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Hcf

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

PPP1CA; protein phosphatase 1 catalytic subunit alpha

6 of 14

176875

PPP1CC; protein phosphatase 1 catalytic subunit gamma

6 of 14

176914

PPP1CB; protein phosphatase 1 catalytic subunit beta

4 of 14

600590

NOONAN SYNDROME-LIKE DISORDER WITH LOOSE ANAGEN HAIR 2; NSLH2

Noonan syndrome-like disorder with loose anagen hair 2

PPEF1; protein phosphatase with EF-hand domain 1

3 of 14

300109

PPEF2; protein phosphatase with EF-hand domain 2

3 of 14

602256

PPP2CA; protein phosphatase 2 catalytic subunit alpha

3 of 14

176915

HOUGE-JANSSENS SYNDROME 3; HJS3

PPP2CB; protein phosphatase 2 catalytic subunit beta

3 of 14

176916

PPP3CA; protein phosphatase 3 catalytic subunit alpha

3 of 14

114105

developmental and epileptic encephalopathy 91

PPP4C; protein phosphatase 4 catalytic subunit

3 of 14

602035

PPP6C; protein phosphatase 6 catalytic subunit

3 of 14

612725

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

esyN Network Diagram

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Pp1-Y1 - CG12620

experimental knowledge based

(Guruharsha et al., 2011)

Pp1-Y1 - CG13994

experimental knowledge based

(Guruharsha et al., 2011)

Pp1-Y1 - I-2

experimental knowledge based

(Guruharsha et al., 2011)

Pp1-Y1 - sds22

experimental knowledge based

(Guruharsha et al., 2011)

Summary of Genetic Interactions

esyN Network Diagram

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Acn

suppressible

Pp1-Y1

(Nandi et al., 2022)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0261399

MIST (protein-protein) - An integrated Molecular Interaction Database

5740113

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

mRNA surveillance pathway

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

A8QI94

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

Y-

Cytogenetic map

Sequence location

Y:9,833..10,786 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

Y-

(de Carvalho, 2001.10.4)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

58098

y¹ v¹; P{TRiP.HMJ22013}attP40

65924

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06189}attP40

NIG-Fly

HMJ22013

y¹ v¹; P{TRiP.HMJ22013}attP40/CyO

VDRC

v110123

P{KK115450}VIE-260B

Genomic Clones (0)

cDNA Clones (0)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0261399

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Sequence of transcript(s) changed in r6 genomic release relative to r5 release.

(FlyBase Genome Annotators, 2014)

New annotation (CG41534) in release 5.2 of the genome annotation.

(Drosophila Heterochromatin Genome Project, 2007)

Relationship to Other Genes

Source for database merge of

Source for merge of: Pp1-Y1 CG41534

(FlyBase, 1996-)

Additional comments

The Pp1-Y1 gene may have been derived from a related phosphoprotein phosphatase gene by retroposition and subsequent tandem duplication.

(Miskei et al., 2011)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG41534

(Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Perkins et al., 2009, Drosophila Heterochromatin Genome Project, 2007)

DmPp1-Y1

(Cohen et al., 2005)

Pp1-Y1

(Chang et al., 2022, Chang et al., 2022, Kotov et al., 2022, Nandi et al., 2022, Bartolo et al., 2021, Lawlor et al., 2021, Zhang et al., 2020, Hoskins et al., 2015, dos Santos, 2014, FlyBase Genome Annotators, 2014, Singh et al., 2014, Guruharsha et al., 2011, Adám et al., 2010, Koerich et al., 2008, Diaz-Castillo and Golic, 2007, Carvalho and Clark, 2005)

Pp1Y1

Name Synonyms

Pp1-Y1

Protein phosphatase 1, Y-linked 1

Secondary FlyBase IDs

FBgn0046699
FBan0041534
FBgn0085674

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 27 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

5740113

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

A8QI94

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

A8QI94

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

5740113/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0261399

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0261399

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG41534

MARRVEL_MODEL - MARRVEL (model organism gene)

5740113

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0261399

DRSC - Results frm RNAi screens

FBgn0261399

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0261399

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

mRNA surveillance pathway

MIST (protein-protein) - An integrated Molecular Interaction Database

5740113

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

A8QI94

References (33)

The following external sites may use different assemblies or annotations than FlyBase.

NA

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