FlyBase Gene Report: Dmel\PQBP1

General Information

Symbol

Dmel\PQBP1

Species

D. melanogaster

Name

Poly-glutamine tract binding protein 1

Annotation Symbol

CG11820

Feature Type

protein_coding_gene

FlyBase ID

FBgn0039270

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

Poly-glutamine tract binding protein 1 (PQBP1) encodes a component of nuclear speckles and cytoplasmic stress granules. It is involved in RNA transcription, RNA splicing, and possibly in protein translation. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Also Known As

PQBP-1, dPQBP1

Key Links

Genomic Location

Cytogenetic map

96B19-96B19

Sequence location

3R:25,065,791..25,066,718 [+]

Recombination map

3-86

RefSeq locus

NT_033777 REGION:25065791..25066718

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (9 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (5 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in microvillus organization

inferred from mutant phenotype

(Wan et al., 2015)

involved_in olfactory learning

inferred from mutant phenotype

(Tamura et al., 2010)

involved_in positive regulation of translation

inferred from direct assay

(Wan et al., 2015)

involved_in rhabdomere development

inferred from mutant phenotype

(Wan et al., 2015)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in mRNA splicing, via spliceosome

inferred by curator from GO:0071011,GO:0071013

(Herold et al., 2009)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

part_of catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in nucleus

inferred from direct assay

(Zhang et al., 2017)

part_of precatalytic spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in rough endoplasmic reticulum

inferred from direct assay

(Wan et al., 2015)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\PQBP1 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 Q9VBY6)

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 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

PQBP1-RA

FBtr0084765

NM_143074

868

231

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

PQBP1-PA

FBpp0084140

27.1

231

10.04

Q9VBY6

NP_651331

AAF56390

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

Q9VBY6

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\PQBP1 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

PQBP1_1

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).

-0.23

Transcript Expression

expression microarray

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

eye

(Xu et al., 2004)

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism | ubiquitous

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

anterior endoderm

(Fisher et al., 2012)

central brain primordium

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

central brain primordium

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

Additional Descriptive Data

Eye-enriched transcripts determined by ratio of expression level in wild-type heads. versus expression level in so heads.

(Xu et al., 2004)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

day 5 of adulthood | male -- day 7 of adulthood | male

spermatozoon

(Dorus et al., 2006)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in nucleus

inferred from direct assay

(Zhang et al., 2017)

part_of precatalytic spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in rough endoplasmic reticulum

inferred from direct assay

(Wan et al., 2015)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\PQBP1 in JBrowse

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

View exonic expression by developmental stage for Dmel\PQBP1

View exonic expression by tissue for Dmel\PQBP1

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0039270

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

43004/tissue=All

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

FBgn0039270

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039270

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

FBgn0039270

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG11820

Flygut - An atlas of the Drosophila adult midgut

FBgn0039270

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of PQBP1

Transgenic constructs containing regulatory region of PQBP1

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 6 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

viable

PQBP1^PL00109

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

PQBP1^GD7395

viable, with Scer\GAL4^Mef2.PR

PQBP1^GD7395

viable, with Scer\GAL4^pnr-MD237

PQBP1^GD7395

viable, with Scer\GAL4^tin.CΔ4

PQBP1^GD7395

Sterility

Allele

fertile

PQBP1^PL00109

Other Phenotypes

Allele

abnormal learning | adult stage

PQBP1^PL00109

abnormal learning | adult stage, with Scer\GAL4^GH146

PQBP1^NIG.11820R

abnormal learning | adult stage, with Scer\GAL4^NP0225

PQBP1^NIG.11820R

abnormal pain response | adult stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

PQBP1^GD7395

short lived, with Scer\GAL4^c747

PQBP1^RNAi.UAS

short lived, with Scer\GAL4^GH146

PQBP1^RNAi.UAS

short lived, with Scer\GAL4^Tub.PU

PQBP1^RNAi.UAS

short lived | semidominant

PQBP1^PL00109

visible, with Scer\GAL4^nub-AC-62

PQBP1^HMJ21589

Phenotype manifest in

Allele

photoreceptor neuron

PQBP1^PL00109

rhabdomere microvillus

PQBP1^PL00109

wing, with Scer\GAL4^nub-AC-62

PQBP1^HMJ21589

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) (1)

Hsap\PQBP1

7 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (1)

Rnor\Pqbp1

6 of 14

Yes

Mus musculus (laboratory mouse) (1)

Mmus\Pqbp1

7 of 14

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\pqbp1

3 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\pqbp1

7 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\pqbp-1.1

9 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP011757

8 of 12

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\AT2G41020

4 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:PQBP1. 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) (1)

cactin

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Renpenning syndrome 1

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 2 )

Allele

Disease

Evidence

References

PQBP1^PL00109

model of Renpenning syndrome

CEA

(Wan et al., 2015, Tamura et al., 2010)

PQBP1^NIG.11820R

model of Renpenning syndrome

CEA

(Tamura et al., 2010)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

PQBP1; polyglutamine binding protein 1

model of Renpenning syndrome

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 1 )

Allele

Disease

Interaction

References

PQBP1^PL00109

model of Renpenning syndrome

is ameliorated by Nmdar1^UAS.cMa

(Tamura et al., 2010)

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?

PQBP1; polyglutamine binding protein 1

7 of 14

POLYGLUTAMINE-BINDING PROTEIN 1; PQBP1

RENPENNING SYNDROME 1; RENS1

Renpenning syndrome

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

PQBP1 - CG34376

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

PQBP1 - Fmr1

anti bait coimmunoprecipitation, western blot, pull down

(Wan et al., 2015)

PQBP1 - Ref1

pull down, peptide massfingerprinting

(Wan et al., 2015)

PQBP1 - Saft

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

PQBP1 - hth

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

PQBP1 - slim

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

PQBP1 - yps

pull down, peptide massfingerprinting, anti bait coimmunoprecipitation, western blot

(Wan et al., 2015)

RNA-protein

Physical Interaction

Assay

References

PQBP1 - Hsc70-3

anti bait coimmunoprecipitation, primer specific pcr

(Wan et al., 2015)

PQBP1 - Tppl

anti bait coimmunoprecipitation, primer specific pcr

(Wan et al., 2015)

PQBP1 - chp

anti bait coimmunoprecipitation, primer specific pcr

(Wan et al., 2015)

PQBP1 - polo

anti bait coimmunoprecipitation, primer specific pcr

(Wan et al., 2015)

PQBP1 - scu

anti bait coimmunoprecipitation, primer specific pcr

(Wan et al., 2015)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

PQBP1

suppressible

Nmdar1

(Tamura et al., 2013, Tamura et al., 2010)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

67925

DroID - A comprehensive database of gene and protein interactions.

FBgn0039270

MIST (genetic) - An integrated Molecular Interaction Database

43004

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

43004

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

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

Spliceosome

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

Q9VBY6

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-86

Cytogenetic map

96B19-96B19

Sequence location

3R:25,065,791..25,066,718 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

96B19-96B19

Limits computationally determined from genome sequence between P{PZ}ssh⁰¹²⁰⁷ and P{lacW}OstStt3^j2D9

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-86

(FlyBase, 2016)

3-85.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (6)

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

Bloomington

54852

y¹ v¹; P{TRiP.HMJ21589}attP40

19390

w^*; P{FRT(w^hs)}2A P{neoFRT}82B PBac{GAL4D,EYFP}PQBP1^PL00109

NIG-Fly

11820R-1

P{NIG.11820R}1

HMJ21589

y¹ v¹; P{TRiP.HMJ21589}attP40

VDRC

v100381

P{KK106109}VIE-260B

v39725

w¹¹¹⁸; P{GD7395}v39725

Genomic Clones (18)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (17)

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

LD40504

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.

FBgn0039270

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0039270

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Wan et al., 2015)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: PQBP1 CG11820

(Tamura et al., 2010)

Nomenclature comments

The gene corresponding to the CG31369 annotation was previously called PQBP-1 (Poly-glutamine tract binding protein 1) in FlyBase, based on the name given in the GenBank accession AJ278495 (which matches part of CG31369 by BLASTN). However, BLAST analysis indicates that CG31369 is not an ortholog of human PQBP-1, and that the D. melanogaster ortholog of human PQBP-1 is CG11820. The gene corresponding to the CG31369 annotation has thus been renamed CG31369 in FlyBase, and the gene corresponding to the CG11820 annotation has been renamed to PQBP1 (as suggested in FBrf0212135).

(FlyBase, 2009-)

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG11820

(Kwon et al., 2016, Ni et al., 2010.12.1, Tamura et al., 2010, Herold et al., 2009, Keleman et al., 2009.8.5, Dorus et al., 2006)

PQBP-1

(Aradska et al., 2015, Duff et al., 2015, Ashwal-Fluss et al., 2014, Kuuluvainen et al., 2014, Japanese National Institute of Genetics, 2012.5.21, LaFerriere et al., 2008)

PQBP1

(Chvilicek et al., 2024, Saha et al., 2022, Wan et al., 2015, Devineni et al., 2011)

dPQBP-1

(Yoshimura et al., 2006)

dPQBP1

(Wan et al., 2015, Tamura et al., 2013, Tamura et al., 2010)

dpqbp1

(Zhang et al., 2017)

Name Synonyms

Poly-glutamine tract binding protein 1

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 35 )

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.

43004

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.

Q9VBY6

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

Q9VBY6

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.

Q9VBY6

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0039270

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

43004/tissue=All

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

FBgn0039270

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

FBgn0039270

FlyMine - An integrated database for Drosophila genomics

FBgn0039270

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

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

dme:Dmel_CG11820

MARRVEL_MODEL - MARRVEL (model organism gene)

43004

Linkouts

BioGRID - A database of protein and genetic interactions.

67925

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0039270

DroID - A comprehensive database of gene and protein interactions.

FBgn0039270

DRSC - Results frm RNAi screens

FBgn0039270

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

PQBP1_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039270

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0039270

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG11820

Flygut - An atlas of the Drosophila adult midgut

FBgn0039270

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0039270

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC014489

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

Spliceosome

MIST (genetic) - An integrated Molecular Interaction Database

43004

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

43004

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

Q9VBY6

References (47)

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

-0.23

Report Sections