FlyBase Gene Report: Dmel\PCID2

General Information

Symbol

Dmel\PCID2

Species

D. melanogaster

Name

PCI domain-containing protein 2

Annotation Symbol

CG7351

Feature Type

protein_coding_gene

FlyBase ID

FBgn0036184

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Required for the export of nuclear mRNAs and involved in mRNA trafficking in the cytoplasm (PubMed:27016737, PubMed:28554770, PubMed:33602059). Component of the nuclear pore complex (NPC)-associated TREX-2/AMEX complex (anchoring and mRNA export complex) which functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket), thereby enabling the export of mRNAs to the cytoplasm through the nuclear pores (PubMed:27016737, PubMed:28554770, PubMed:33602059). Within the complex, specifically promotes the association of factors involved in regulating nuclear mRNA export, such as Moe, sbr/NXF1 and the ORC complex, to the mRNPs particles (PubMed:27016737, PubMed:28554770, PubMed:33602059). In the cytoplasm, functions independently of its role in the TREX-2/AMEX complex, to promote cytoplasmic mRNA trafficking together with nudC (PubMed:33602059). Associates with translationally active polysomes (PubMed:18086857). (UniProt, Q9VTL1)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

68C15-68C15

Sequence location

3L:11,626,441..11,627,715 [+]

Recombination map

3-36

RefSeq locus

NT_037436 REGION:11626441..11627715

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 (11 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables protein binding

inferred from physical interaction with UniProtKB:Q9U1H9

(Farny et al., 2008)

inferred from physical interaction with UniProtKB:Q7K2L1

(Kopytova et al., 2016)

inferred from physical interaction with UniProtKB:Q9W102

(Kopytova et al., 2016)

enables protein domain specific binding

inferred from physical interaction with UniProtKB:P46150

(Kristó et al., 2017)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables double-stranded DNA binding

inferred from electronic annotation with InterPro:IPR045114

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000296424

(GO Reference Genome Project, 2011-)

enables RNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000296424

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR045114

(InterPro Project Members, 2004-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in mRNA export from nucleus

inferred from direct assay

(Farny et al., 2008)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

involved_in poly(A)+ mRNA export from nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000296424

(GO Reference Genome Project, 2011-)

involved_in post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery

inferred from biological aspect of ancestor with PANTHER:PTN000296424

(GO Reference Genome Project, 2011-)

involved_in transcription elongation by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN000296424

(GO Reference Genome Project, 2011-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Farny et al., 2008)

located_in nucleus

inferred from direct assay

(Kopytova et al., 2016, Farny et al., 2008)

part_of transcription export complex 2

inferred from direct assay

(Kopytova et al., 2016)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of transcription export complex 2

inferred from biological aspect of ancestor with PANTHER:PTN000296424

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

TRANSCRIPTION EXPORT COMPLEX-2

Protein Family (UniProt)

Belongs to the CSN12 family. (Q9VTL1)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

TRANSCRIPTION EXPORT COMPLEX-2 -: TREX-2 is a multisubunit complex required for mRNA export through the nuclear pore. TREX-2 colocalizes with the nuclear pore complex at the nuclear periphery. (Adapted from FBrf0232523 and FBrf0200574).

Protein Function (UniProtKB)

(UniProt, Q9VTL1)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\PCID2 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 Q9VTL1)

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 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

PCID2-RA

FBtr0076102

NM_140229

1275

395

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

PCID2-PA

FBpp0075833

45.2

395

8.51

Q9VTL1

NP_648486

AAF50037

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

Subunit Structure (UniProtKB)

Component of the nuclear pore complex (NPC)-associated TREX-2/AMEX complex (anchoring and mRNA export complex), composed of e(y)2, xmas and PCID2 (PubMed:27016737). Interaction between the TREX-2/AMEX complex and the ORC complex is required for ORC localization to mRNPs, and consequently mRNA export (PubMed:27016737). Within the TREX-2/AMEX-ORC complex, interacts with Orc3 and Orc4 (PubMed:27016737). Interacts with sbr/NXF1 (PubMed:18086857). Interacts with Moe (PubMed:28554770). Interacts with nudC; required to maintain stability in the cytoplasm (PubMed:33602059).

(UniProt, Q9VTL1)

Post Translational Modification

Mono- and poly-ubiquitinated.

(UniProt, Q9VTL1)

Domain

PCI domain is required for interaction with polysomes but not the interaction with sbr.

(UniProt, Q9VTL1)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VTL1

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\PCID2 using the Feature Mapper tool.

External Data

Crossreferences

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

PCID2_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).

0.33

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Farny et al., 2008)

located_in nucleus

inferred from direct assay

(Kopytova et al., 2016, Farny et al., 2008)

part_of transcription export complex 2

inferred from direct assay

(Kopytova et al., 2016)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\PCID2 in JBrowse

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

View exonic expression by developmental stage for Dmel\PCID2

View exonic expression by tissue for Dmel\PCID2

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

FBgn0036184

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

39306/tissue=All

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

FBgn0036184

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0036184

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

FBgn0036184

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

CG7351

Flygut - An atlas of the Drosophila adult midgut

FBgn0036184

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 ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of PCID2

Transgenic constructs containing regulatory region of PCID2

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

PCID2^GD12209

viable, with Scer\GAL4^Mef2.PR

PCID2^GD12209

viable, with Scer\GAL4^pnr-MD237

PCID2^GD12209

viable, with Scer\GAL4^tin.CΔ4

PCID2^GD12209

Sterility

Allele

female fertile, with Scer\GAL4^nanos.PG

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) (3)

Hsap\PCID2

13 of 14

Yes

Hsap\COPS3

1 of 14

Hsap\PSMD3

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) (3)

Rnor\Pcid2

14 of 14

Yes

Rnor\Cops3

1 of 14

Rnor\Psmd3

1 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Pcid2

13 of 14

Yes

Mmus\Cops3

1 of 14

Mmus\Psmd3

1 of 14

Xenopus tropicalis (Western clawed frog) (3)

Xtro\pcid2

7 of 13

Yes

Xtro\cops3

1 of 13

Xtro\mtg2

1 of 13

Danio rerio (Zebrafish) (3)

Drer\pcid2

14 of 14

Yes

Drer\cops3

1 of 14

Drer\psmd3

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (3)

Cele\C27F2.10

14 of 14

Yes

Cele\C27F2.7

1 of 14

Yes

Cele\rpn-3

1 of 14

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP008498

12 of 12

Yes

Agam\AgaP_AGAP006445

1 of 12

Agam\PSMD3_ANOGA

1 of 12

Arabidopsis thaliana (thale-cress) (4)

Atha\EER5

13 of 13

Yes

Atha\AT1G75990

1 of 13

Atha\COP13

1 of 13

Atha\EMB2719

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\YJR084W

9 of 13

Yes

Scer\THP1

4 of 13

Yes

Scer\RPN3

1 of 13

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\SPAC1B3.08

11 of 12

Yes

Spom\SPBC1105.07c

4 of 12

Yes

Spom\rpn3

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:PCID2. 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) (2)

CSN3

1 of 13

Rpn3

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?

PCID2; PCI domain containing 2

13 of 14

613713

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

PCID2 - Cbp80

anti bait coimmunoprecipitation, western blot

(Popova et al., 2016)

PCID2 - DCTN1-p150

anti bait coimmunoprecipitation, western blot

(Glukhova et al., 2021)

PCID2 - Moe

anti tag coimmunoprecipitation, western blot

(Kristó et al., 2017)

PCID2 - Orc3

anti tag coimmunoprecipitation, anti tag western blot

(Kopytova et al., 2016)

PCID2 - Orc4

anti tag coimmunoprecipitation, anti tag western blot

(Kopytova et al., 2016)

PCID2 - RpLP0

cosedimentation, anti tag western blot

(Farny et al., 2008)

PCID2 - Sem1

two hybrid

(Hu et al., 2017.6.13)

PCID2 - e(y)2

anti bait coimmunoprecipitation, western blot, peptide massfingerprinting

(Kopytova et al., 2016, Popova et al., 2016)

PCID2 - nudC

pull down, molecular weight estimation by staining, anti bait coimmunoprecipitation, western blot, Identification by mass spectrometry

(Glukhova et al., 2021)

PCID2 - sbr

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, anti tag western blot

(Popova et al., 2016, Farny et al., 2008)

PCID2 - thoc5

anti bait coimmunoprecipitation, western blot

(Popova et al., 2016)

PCID2 - xmas

anti tag coimmunoprecipitation, anti tag western blot, anti bait coimmunoprecipitation, western blot

(Vdovina et al., 2023, Popova et al., 2016)

RNA-protein

Physical Interaction

Assay

References

PCID2 - Ras64B

pull down, western blot, electrophoretic mobility shift assay, autoradiography, anti bait coimmunoprecipitation, quantitative reverse transcription pcr

(Vdovina et al., 2023, Vdovina et al., 2023, Glukhova et al., 2021)

PCID2 - βTub56D

pull down, western blot, anti bait coimmunoprecipitation, quantitative reverse transcription pcr

(Glukhova et al., 2021, Popova et al., 2016)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

(UniProt, Q9VTL1 )

Linkouts

BioGRID - A database of protein and genetic interactions.

64668

DroID - A comprehensive database of gene and protein interactions.

FBgn0036184

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

39306

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-36

Cytogenetic map

68C15-68C15

Sequence location

3L:11,626,441..11,627,715 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

68C15-68C15

Limits computationally determined from genome sequence between P{PZ}l(3)01239⁰¹²³⁹&P{lacW}l(3)01239^j9B4 and P{PZ}CycA⁰²⁴⁶¹&P{PZ}CycA⁰³⁹⁴⁶

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-36

(FlyBase, 2016)

3-30.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

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

Bloomington

28104

y¹ w^*; P{EP}PCID2^G18683

7351R-1

v108871

v27966

w¹¹¹⁸; P{GD12209}v27966

v342782

P{hsFLP}1, y1 w1118; P{HD_CFD01823}attP40/CyO-GFP

Genomic Clones (16)

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

cDNA Clones (7)

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

LD40777

Other clones

DPiM_LD40777

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.

FBgn0036184

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

31070

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0036184

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Glukhova et al., 2021, Kopytova et al., 2016)

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: PCID2 CG7351

(Farny et al., 2008)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG7351

(Çiçek et al., 2016, Hosono et al., 2015, Lin et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Lim et al., 2011, Keleman et al., 2009.8.5, Farny et al., 2008)

PCID2

(Vdovina et al., 2024, Vdovina et al., 2023, Vdovina et al., 2023, Abbott et al., 2020, Hu et al., 2017.6.13, Kristó et al., 2017, Kopytova et al., 2016, Popova et al., 2016, Czech et al., 2013)

dmPCID2

(Farny et al., 2008)

Name Synonyms

CG7351

Drosophila melanogaster PCID2

(Farny et al., 2008)

PCI domain-containing protein 2

(Lim et al., 2011)

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 ( 33 )

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.

39306

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.

Q9VTL1

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9VTL1

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.

Q9VTL1

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0036184

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

39306/tissue=All

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

FBgn0036184

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

FBgn0036184

FlyMine - An integrated database for Drosophila genomics

FBgn0036184

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

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

dme:Dmel_CG7351

MARRVEL_MODEL - MARRVEL (model organism gene)

39306

Linkouts

BioGRID - A database of protein and genetic interactions.

64668

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

FBgn0036184

DroID - A comprehensive database of gene and protein interactions.

FBgn0036184

DRSC - Results frm RNAi screens

FBgn0036184

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

PCID2_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0036184

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0036184

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

CG7351

Flygut - An atlas of the Drosophila adult midgut

FBgn0036184

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

TC000849

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

39306

References (40)

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

0.33

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