FlyBase Gene Report: Dmel\CG42788

General Information

Symbol

Dmel\CG42788

Species

D. melanogaster

Name

Annotation Symbol

CG42788

Feature Type

protein_coding_gene

FlyBase ID

FBgn0261859

Gene Model Status

Current

Stock Availability

18 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

88E1-88E2

Sequence location

3R:15,095,957..15,131,926 [-]

Recombination map

3-56

RefSeq locus

NT_033777 REGION:15095957..15131926

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 (2 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 (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in signal transduction

inferred from biological aspect of ancestor with PANTHER:PTN000817101

(GO Reference Genome Project, 2011-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000817101

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\CG42788 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 Q9VFD3)

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 5.53

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

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

CG42788-RB

FBtr0303486

NM_169609

6686

1560

CG42788-RC

FBtr0303485

NM_001202293

6683

1559

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

CG42788-PB

FBpp0292538

168.3

1560

6.61

FBpp0292537

168.2

1559

6.61

A0A0B4JDC8

NP_001189222

ADV37313

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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\CG42788 using the Feature Mapper tool.

External Data

Crossreferences

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

CG42788_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).

-1.02

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 9 -- 10

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 11 -- 12

fat body primordium

Comment: reported as fat body specific anlage

(Fisher et al., 2012)

fat body/gonad primordium

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic/larval fat body

(Fisher et al., 2012)

larval muscle system

(Fisher et al., 2012)

gonad

(Fisher et al., 2012)

Additional Descriptive Data

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)

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\CG42788 in JBrowse

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

View exonic expression by developmental stage for Dmel\CG42788

View exonic expression by tissue for Dmel\CG42788

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

FBgn0261859

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

41817/tissue=All

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

FBgn0261859

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

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

FBgn0261859

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

Flygut - An atlas of the Drosophila adult midgut

FBgn0261859

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 10 )

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 CG42788

Transgenic constructs containing regulatory region of CG42788

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 8 )

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

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

viable, with Scer\GAL4^tin.CΔ4

CG42788^GD8865

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) (29)

Hsap\FRMPD4

8 of 14

Yes

Hsap\FRMPD1

6 of 14

Yes

Hsap\FRMPD3

5 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 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) (20)

Rnor\Frmpd4

7 of 14

Yes

Rnor\Frmpd1

4 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (22)

Mmus\Frmpd4

7 of 14

Yes

Mmus\Frmpd1

6 of 14

Yes

Mmus\Frmpd3

5 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (18)

Xtro\frmpd4

5 of 13

Yes

Xtro\frmpd1

4 of 13

Yes

Xtro\frmpd3

2 of 13

Yes

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

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (33)

Drer\frmpd1b

6 of 14

Yes

Drer\frmpd3

6 of 14

Yes

Drer\tlr7

6 of 14

Yes

Drer\frmpd4

2 of 14

Yes

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

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Drer\radil

1 of 14

Yes

Drer\si:ch73-281f12.4

1 of 14

Yes

Drer\si:ch211-176g6.2

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (7)

Cele\frm-8

8 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (7)

Agam\AgaP_AGAP003128

11 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

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:CG42788. 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) (8)

Magi

2 of 13

baz

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

yki

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 ( 1 )

Human Ortholog

Disease

Evidence

References

FRMPD4; FERM and PDZ domain containing 4

model of non-syndromic X-linked intellectual disability 104

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 1 )

Allele

Disease

Interaction

References

CG42788^GD8865

ameliorates tauopathy

modeled by Hsap\MAPT^R406W.UAS

(Butzlaff et al., 2015)

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?

FRMPD4; FERM and PDZ domain containing 4

8 of 14

300838

INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 104; XLID104

non-syndromic X-linked intellectual disability 104

FRMPD1; FERM and PDZ domain containing 1

6 of 14

616919

FRMPD3; FERM and PDZ domain containing 3

5 of 14

301005

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

CG42788 - drk

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

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

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0261859

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

41817

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

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

Q9VFD3

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-56

Cytogenetic map

88E1-88E2

Sequence location

3R:15,095,957..15,131,926 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

88E1-88E2

Limits computationally determined from genome sequence between P{EP}CG33967^EP666 and P{lacW}Hsc70-4^L3929

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-56

(FlyBase, 2016)

3-55.6

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (18)

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

Bloomington

31556

y¹ v¹; P{TRiP.JF01124}attP2

53448

y¹ w^*; Mi{MIC}CG42788^MI10043

60756

y¹ w^*; Mi{MIC}CG42788^MI02203

22905

y¹ w^67c23; Mi{ET1}CG42788^MB00815

602856

y¹ w^*; TI{CRIMIC.TG4.2}CG42788^{CR02177-TG4.2}

Kyoto

123787

w¹¹¹⁸; P{RS3}CG42788^CB-5737-3

124173

w¹¹¹⁸; P{RS3}CG42788^CB-6669-3

31304R-2

31304R-3

v100279

v108180

v341756

P{hsFLP}1, y¹ w¹¹¹⁸; P{HD_CFD00878}attP40/CyO-GFP

More stocks available...

Genomic Clones (32)

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

cDNA Clones (16)

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

MIP05125

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.

FBgn0261859

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0261859

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

Area matching Drosophila EST AA696498.

(Davies, 2001.3.15)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG31304 CG6934

(FlyBase Genome Annotators, 2010)

Source for merge of: CG6934 anon-WO0118547.79

(FlyBase, 1996-)

Source for merge of: CG18442 CG6960

(FlyBase Genome Annotators, 2002-2003)

Additional comments

Annotations CG31304 and CG6934 merged as CG42788 in release 5.28 of the genome annotation.

(FlyBase Genome Annotators, 2010)

Annotations CG18442 and CG6960 merged as CG31304 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Source for merge of CG6934 anon-WO0118547.79 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

CG18442

CG31304

(Japanese National Institute of Genetics, 2012.5.21, Keleman et al., 2009.8.5)

CG42788

(Praschberger et al., 2023, Huang et al., 2021, Kumar et al., 2021, Kvon et al., 2021, Gene Disruption Project members, 2018-, Cannavò et al., 2016, Butzlaff et al., 2015, Toshima et al., 2014, Short and Lazzaro, 2013, Friedman et al., 2011, FlyBase Genome Annotators, 2010, Ni et al., 2010.12.1, Ni et al., 2008)

CG6934

(Ashwal-Fluss et al., 2014, Ou et al., 2011, Ni et al., 2010.12.1, Keleman et al., 2009.8.5)

CG6960

anon-WO0118547.79

Name Synonyms

Secondary FlyBase IDs

FBgn0051304
FBgn0038287
FBgn0038288
FBgn0061647
FBgn0038289

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 46 )

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.

41817

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.

Q9VFD3

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.

Q9VFD3

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0261859

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

41817/tissue=All

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

FBgn0261859

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

FBgn0261859

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

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

dme:Dmel_CG42788

MARRVEL_MODEL - MARRVEL (model organism gene)

41817

Linkouts

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

FBgn0261859

DroID - A comprehensive database of gene and protein interactions.

FBgn0261859

DRSC - Results frm RNAi screens

FBgn0261859

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

CG42788_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0261859

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

Flygut - An atlas of the Drosophila adult midgut

FBgn0261859

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

TC004369

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

41817

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

Q9VFD3

References (53)

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

-1.02

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