FlyBase Gene Report: Dmel\pcx

General Information

Symbol

Dmel\pcx

Species

D. melanogaster

Name

pecanex

Annotation Symbol

CG3443

Feature Type

protein_coding_gene

FlyBase ID

FBgn0003048

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

Involved in neurogenesis. (UniProt, P18490)

Contribute a Gene Snapshot for this gene.

All Summaries

Also Known As

fs(1)pcx, EG:30B8.4 , mel(1)R1, fs(1)M10

Key Links

Genomic Location

Cytogenetic map

2F1-2F1

Sequence location

X:2,225,296..2,238,045 [+]

Recombination map

1-0.9

RefSeq locus

NC_004354 REGION:2225296..2238045

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 (3 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in endoplasmic reticulum organization

inferred from mutant phenotype

(Yamakawa et al., 2012)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in endoplasmic reticulum organization

inferred from biological aspect of ancestor with PANTHER:PTN002644407

(GO Reference Genome Project, 2011-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in endoplasmic reticulum

inferred from direct assay

(Yamakawa et al., 2012)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in endoplasmic reticulum

inferred from biological aspect of ancestor with PANTHER:PTN002644407

(GO Reference Genome Project, 2011-)

located_in membrane

inferred from electronic annotation with InterPro:IPR007735

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the pecanex family. (P18490)

Protein Signatures (InterPro)

Summaries

Protein Function (UniProtKB)

Involved in neurogenesis.

(UniProt, P18490)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

fs(1)A387

Embryos fail late in development; some rescue by fertilization with sperm carrying normal allele.

pcx: pecanex

Maternal-effect-lethal mutation; homozygous mutant females crossed to mutant males produce lethal embryos showing hypertrophy of the central nervous system at the expense of the epidermis, a small patch of dorsal cuticle remaining but no ventral cuticle. This embryonic phenotype (as well as the reduced eye phenotype of viable pcx adults) resembles that of amx. Homozygous pcx lethal embryos can be rescued genetically; some mutant females (but not pcx1 homozygotes) crossed to wild-type males produce viable adult pcx/+ female offspring (Romans et al., 1976; Perrimon et al., 1984); the pcx/Y male offspring are lethal. pcx/+ heterozygous females, which are fertile, crossed to viable pcx/Y males (also fertile) produce viable adult males (pcx/Y and +/Y) and viable adult females (pcx/pcx and pcx/+) (Romans et al., 1976). Homozygous pcx lethal embryos can be partially rescued almost up to hatching by preblastoderm microinjection of wild-type or amx ooplasm (La Bonne and Mahowald, 1985a). Germ line clonal analysis demonstrates the germ-line dependency of the pcx embryonic lethal phenotype (Perrimon et al., 1984).

Summary (Interactive Fly)

a component of the Notch signaling pathway - a transmembrane protein required for ER function - potentially required in Notch signal-receiving cells for processing of Notch protein

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\pcx 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 P18490)

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 5.51

Gene model reviewed during 5.45

Low-frequency RNA-Seq exon junction(s) not annotated.

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated.

Gene model reviewed during 5.53

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

pcx-RC

FBtr0332381

NM_001272253

12107

3413

pcx-RE

FBtr0342766

NM_001272254

12119

3417

pcx-RF

FBtr0344153

NM_080306

12023

3413

Additional Transcript Data and Comments

Reported size (kB)

9, 3.7, 2.3 (northern blot)

(LaBonne et al., 1989)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

pcx-PC

FBpp0304655

365.3

3413

6.03

FBpp0309618

365.8

3417

6.03

FBpp0310566

365.3

3413

6.03

P18490

NP_525045

AAF45756

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

3413 aa isoforms: pcx-PC, pcx-PF

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

2483 aa fragment marked as 5' end in GenBank contains all of M25662

(FlyBase, 1992-)

1938 aa fragment contained within M74329

(FlyBase, 1992-)

No significant similarity was found between the

pcx protein sequence and any other protein.

(LaBonne et al., 1989)

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\pcx using the Feature Mapper tool.

External Data

Crossreferences

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

pcx_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).

-0.41

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 4

organism | ubiquitous | uniform

Comment: maternally deposited

(Yamakawa et al., 2012)

embryonic stage 10 -- 14

organism | ubiquitous

(Yamakawa et al., 2012)

Additional Descriptive Data

pcx transcript is strongly expressed in pre-blastoderm and blastoderm embryos; expression levels decrease at later embryonic stages. pcx transcript is not detected in imaginal discs.

(Yamakawa et al., 2012)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in endoplasmic reticulum

inferred from direct assay

(Yamakawa et al., 2012)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\pcx in JBrowse

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

View exonic expression by developmental stage for Dmel\pcx

View exonic expression by tissue for Dmel\pcx

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

31204/tissue=All

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

FBgn0003048

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003048

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

FBgn0003048

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

CG3443

Flygut - An atlas of the Drosophila adult midgut

FBgn0003048

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 16 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of pcx

Transgenic constructs containing regulatory region of pcx

Aberrations (Deficiencies and Duplications) ( 20 )

Inferred from experimentation ( 20 )

Gene duplicated in

Dp(1;3)w^vco

(Perrimon et al., 1985)

Dp(1;Y)w⁺303

(Perrimon et al., 1985)

Inferred from location ( 26 )

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

lethal | maternal effect

pcx¹

lethal | rescuable maternal effect

lethal - all die during embryonic stage | maternal effect | recessive

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

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

viable, with Scer\GAL4^tin.CΔ4

Sterility

Allele

female sterile | recessive

Other Phenotypes

Allele

neurogenic phenotype | embryonic stage | maternal effect

pcx³

neurogenic phenotype | embryonic stage | maternal effect (with Df(1)ED6574)

pcx³

some die during embryonic stage | recessive | maternal effect | recessive

visible, with Scer\GAL4^pnr-MD237

pcx^GD3203

wild-type

pcx^+tcos9

Phenotype manifest in

Allele

chaeta | increased number, with Scer\GAL4^pnr-MD237

pcx^GD3203

egg | maternal effect

embryonic/first instar larval cuticle | ventral

pcx¹

endoplasmic reticulum | maternal effect

pcx³

presumptive embryonic/larval central nervous system

pcx¹

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\PCNX3

11 of 14

Yes

Hsap\PCNX1

10 of 14

Yes

Hsap\PCNX2

10 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) (3)

Rnor\Pcnx3

11 of 14

Yes

Rnor\Pcnx1

10 of 14

Yes

Rnor\Pcnx2

10 of 14

Yes

Mus musculus (laboratory mouse) (3)

Mmus\Pcnx3

11 of 14

Yes

Mmus\Pcnx

10 of 14

Yes

Mmus\Pcnx2

9 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\pcnx1

8 of 13

Yes

Xtro\pcnx2

5 of 13

Yes

Xtro\rtn4ip1

2 of 13

Danio rerio (Zebrafish) (3)

Drer\pcnx1

10 of 14

Yes

Drer\pcnx2

10 of 14

Yes

Drer\pcnx3

9 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\B0511.12

9 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP003872

9 of 12

Yes

Arabidopsis thaliana (thale-cress) (0)

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:pcx. 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) (0)

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?

11 of 14

10 of 14

10 of 14

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

RNA-RNA

Physical Interaction

Assay

References

pcx - mir-124

quantitative reverse transcription pcr

(Sun et al., 2012)

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

pcx

suppressible

Hsc70-3

(Yamakawa et al., 2012)

pcx

suppressible

(Yamakawa et al., 2012)

pcx

suppressible

Ofut1

(Yamakawa et al., 2012)

pcx

suppressible

Xbp1

(Yamakawa et al., 2012)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

57742

DroID - A comprehensive database of gene and protein interactions.

FBgn0003048

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

31204

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

1-0.9

Cytogenetic map

2F1-2F1

Sequence location

X:2,225,296..2,238,045 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

2F1-2F1

Limits computationally determined from genome sequence between P{EP}EP1460&P{EP}CG2924^EP1596 and P{EP}EP1606

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

2E-2F

(determined by in situ hybridisation)

(LaBonne et al., 1989)

Experimentally Determined Recombination Data

Location

1-0.9

(FlyBase, 2016)

1-0.2

(Comeron et al., 2012)

(Mohler, 1977)

Left of (cM)

(Mohler, 1977)

Right of (cM)

(Mohler, 1977)

Notes

Stocks and Reagents

Stocks (6)

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

Bloomington

62780

PBac{IT.GAL4}pcx^0323-G4 w¹¹¹⁸/FM7a

20674

y¹ P{EPgy2}pcx^EY11346 w^67c23

28552

y¹ v¹; P{TRiP.HM05038}attP2/TM3, Sb¹

4592

y¹ pcx³ cv¹ v¹ f¹/FM6

VDRC

v29893

w¹¹¹⁸; P{GD15328}v29893

v45684

w¹¹¹⁸; P{GD12502}v45684

Genomic Clones (16)

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

cDNA Clones (25)

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

SD01552

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.

FBgn0003048

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0003048

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Mutant embryos exhibit hypertrophy of the nervous system and can be rescued by P element carrying wild type genomic region.

(Haenlin et al., 1985)

Germ line clone analysis establishes that the pcx phenotype is germ line-dependent.

(Perrimon et al., 1984)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: pcx CG3443

(Deng, 1999.11)

Nomenclature comments

Etymology

Because of the mutant phenotype similarities to almondex this locus has been named "pecanex".

(Perrimon et al., 1984)

Named for its phenotypic resemblance to amx.

Synonyms and Secondary IDs (18)

Reported As

Symbol Synonym

CG3443

(Perkins et al., 2009, Benos, 2000.12.13)

DMPCX

(Schug et al., 1998)

EG:30B8.4

(Benos et al., 2001, Benos, 2000.12.13, Benos, 2000.12.13)

fs(1)12-1012

fs(1)12-1743

fs(1)12-2135

fs(1)12-3014

fs(1)12-3102

fs(1)12-4169

fs(1)14-1153

fs(1)14-567

fs(1)A387

fs(1)M10

(Mohler and Carroll, 1984, Mohler, 1977)

fs(1)pcx

(Gandhi et al., 1992, Perrimon et al., 1985, Perrimon et al., 1984)

mel(1)R

mel(1)R1

(Mohler and Carroll, 1984)

pcx

(Peng et al., 2024, Das et al., 2020, Parker et al., 2020, Yamakawa et al., 2018, Clandinin and Owens, 2016-, Sun et al., 2012, Yamakawa et al., 2012)

Name Synonyms

pecanex

(Ryoo, 2015, Yamakawa et al., 2012, Mudiganti et al., 2010, Wesley, 1999, Edwards et al., 1997)

Secondary FlyBase IDs

FBgn0000752
FBgn0026853

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 49 )

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.

31204

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.

P18490

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

P18490

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.

P18490

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

31204/tissue=All

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

FBgn0003048

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

FBgn0003048

FlyMine - An integrated database for Drosophila genomics

FBgn0003048

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

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

dme:Dmel_CG3443

MARRVEL_MODEL - MARRVEL (model organism gene)

31204

Linkouts

BioGRID - A database of protein and genetic interactions.

57742

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

FBgn0003048

DroID - A comprehensive database of gene and protein interactions.

FBgn0003048

DRSC - Results frm RNAi screens

FBgn0003048

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

pcx_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003048

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0003048

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

CG3443

Flygut - An atlas of the Drosophila adult midgut

FBgn0003048

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

TC007308

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

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

31204

References (68)

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

-0.41

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