FlyBase Gene Report: Dmel\Gdap1

General Information

Symbol

Dmel\Gdap1

Species

D. melanogaster

Name

Gdap1

Annotation Symbol

CG4623

Feature Type

protein_coding_gene

FlyBase ID

FBgn0035587

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

Gdap1 (Gdap1) encodes a transmembrane protein of the outer mitochondrial membrane. Dysregulation of Gdap1 expression has been related to mitochondrial dynamics, oxidative stress and neuromuscular degeneration. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Also Known As

dGdap1

Key Links

Genomic Location

Cytogenetic map

64C7-64C7

Sequence location

3L:5,141,953..5,144,317 [+]

Recombination map

3-13

RefSeq locus

NT_037436 REGION:5141953..5144317

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 (5 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in mitochondrion organization

inferred from mutant phenotype

(López Del Amo et al., 2015)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in mitochondrial fission

inferred from biological aspect of ancestor with PANTHER:PTN002544728

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with UniProtKB:Q8TB36

(López Del Amo et al., 2015)

involved_in mitochondrial fusion

inferred from biological aspect of ancestor with PANTHER:PTN002544728

(GO Reference Genome Project, 2011-)

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 mitochondrial outer membrane

inferred from biological aspect of ancestor with PANTHER:PTN002544728

(GO Reference Genome Project, 2011-)

located_in mitochondrion

inferred from sequence or structural similarity with UniProtKB:Q8TB36

(López Del Amo et al., 2015)

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\Gdap1 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 Q9VRJ3)

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

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

Gene model reviewed during 5.45

Gene model reviewed during 5.53

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Gdap1-RA

FBtr0077167

NM_139688

1597

327

Gdap1-RB

FBtr0331805

NM_001274508

1594

326

Gdap1-RC

FBtr0344225

NM_001300010

1511

320

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

Gdap1-PA

FBpp0076870

37.6

327

8.25

FBpp0304190

37.6

326

8.25

FBpp0310631

36.9

320

7.82

X2JAP0

NP_001286939

AHN57964

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\Gdap1 using the Feature Mapper tool.

External Data

Crossreferences

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

CG4623_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).

0.14

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 13 -- 16

embryonic epipharynx

(Fisher et al., 2012)

embryonic hypopharynx

(Fisher et al., 2012)

embryonic Malpighian tubule

(Fisher et al., 2012)

embryonic midgut chamber

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

distribution deduced from reporter or direct label

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 17

embryonic/larval midgut

(López Del Amo et al., 2015)

embryonic/larval hindgut

(López Del Amo et al., 2015)

embryonic/larval Malpighian tubule

(López Del Amo et al., 2015)

embryonic/larval anal pad

(López Del Amo et al., 2015)

larval antenno-maxillary sensory complex

(López Del Amo et al., 2015)

first instar larval stage

embryonic/larval midgut

(López Del Amo et al., 2015)

embryonic/larval hindgut

(López Del Amo et al., 2015)

embryonic/larval Malpighian tubule

(López Del Amo et al., 2015)

embryonic/larval anal pad

(López Del Amo et al., 2015)

larval antenno-maxillary sensory complex

(López Del Amo et al., 2015)

adult stage

retina

(López Del Amo et al., 2015)

indirect flight muscle cell

(López Del Amo et al., 2015)

adult gut

(López Del Amo et al., 2015)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Expression is not detected until late embryonic and first larval instar stages. It is then observed in midgut, hindgut, malpighian

(López Del Amo et al., 2015)

tubules, anal pads and antenno-maxillary sense organs. Expression is detected in adults most prominently in the gut and also in the retina and indirect flight muscles.

(López Del Amo et al., 2015)

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\Gdap1 in JBrowse

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

View exonic expression by developmental stage for Dmel\Gdap1

View exonic expression by tissue for Dmel\Gdap1

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

FBgn0035587

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

38597/tissue=All

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

FBgn0035587

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0035587

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

FBgn0035587

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

CG4623

Flygut - An atlas of the Drosophila adult midgut

FBgn0035587

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Gdap1

Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 2 )

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 Gdap1

Transgenic constructs containing regulatory region of Gdap1

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)Exel6103

(Ryder, 2004.4.26)

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

Gdap1^GD10713

viable, with Scer\GAL4^Mef2.PR

Gdap1^GD10713

viable, with Scer\GAL4^pnr-MD237

Gdap1^GD10713

viable, with Scer\GAL4^tin.CΔ4

Gdap1^GD10713

Other Phenotypes

Allele

abnormal neuroanatomy | adult stage | progressive, with Scer\GAL4^GMR.PU

visible, with Scer\GAL4^Mhc.PU

Phenotype manifest in

Allele

capitate projection, with Scer\GAL4^GMR.PU

eye photoreceptor cell | progressive, with Scer\GAL4^GMR.PU

indirect flight muscle cell, with Scer\GAL4^Mhc.PU

mitochondrion, with Scer\GAL4^GMR.PU

mitochondrion, with Scer\GAL4^Mhc.PU

optic cartridge, with Scer\GAL4^GMR.PU

rhabdomere, with Scer\GAL4^GMR.PU

wing, with Scer\GAL4^Mhc.PU

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) (10)

Hsap\GDAP1

12 of 14

Yes

Hsap\GDAP1L1

11 of 14

Yes

2 of 14

2 of 14

2 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) (7)

Rnor\Gdap1

12 of 14

Yes

Rnor\Gdap1l1

11 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (8)

Mmus\Gdap1l1

11 of 14

Yes

Mmus\Gdap1

11 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (5)

Xtro\gdap1l1

10 of 13

Yes

Xtro\gdap1

10 of 13

Yes

Xtro\gsta4

1 of 13

Xtro\gstt1-like.2

1 of 13

Xtro\LOC100498493

1 of 13

Danio rerio (Zebrafish) (4)

Drer\gdap1

12 of 14

Yes

Drer\gdap1l1

11 of 14

Yes

Drer\gstr

2 of 14

Drer\gstt2

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (5)

Cele\gst-43

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (29)

Agam\AgaP_AGAP006132

12 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (25)

Atha\AT1G77290

9 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

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

Saccharomyces cerevisiae (Brewer's yeast) (5)

Scer\CAM1

2 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\gst1

1 of 12

Yes

Spom\gst2

1 of 12

Yes

Escherichia coli (enterobacterium) (3)

Ecol\gstB

1 of 11

Yes

Ecol\sspA

1 of 11

Yes

Ecol\yfcG

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Gdap1. 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) (38)

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

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

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

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Charcot-Marie-Tooth disease, GDAP1-related

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 2 )

Allele

Disease

Evidence

References

Gdap1^UAS.cLa

model of Charcot-Marie-Tooth disease

CEA

(López Del Amo et al., 2017, López Del Amo et al., 2015)

Gdap1^GD10713

model of Charcot-Marie-Tooth disease

CEA

(López Del Amo et al., 2017, López Del Amo et al., 2015)

Potential Models Based on Orthology ( 4 )

Human Ortholog

Disease

Evidence

References

GDAP1; ganglioside induced differentiation associated protein 1

model of Charcot-Marie-Tooth disease recessive intermediate A

IEA

(FlyBase, 2019-)

model of Charcot-Marie-Tooth disease axonal type 2K

IEA

(FlyBase, 2019-)

model of autosomal recessive axonal Charcot-Marie-Tooth disease with vocal cord paresis

IEA

(FlyBase, 2019-)

model of Charcot-Marie-Tooth disease type 4A

IEA

(FlyBase, 2019-)

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?

GDAP1; ganglioside induced differentiation associated protein 1

12 of 14

GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1; GDAP1

GDAP1L1; ganglioside induced differentiation associated protein 1 like 1

11 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.

Dmel gene

Ortholog showing functional complementation

Supporting References

Gdap1

Hsap\GDAP1

(López Del Amo et al., 2015)

Interactions

Summary of Physical Interactions

Interaction Browsers

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Marf

suppressible

Gdap1

(López Del Amo et al., 2015)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

64065

DroID - A comprehensive database of gene and protein interactions.

FBgn0035587

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

38597

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class I peroxisomal membrane protein import

Class of Gene

gene_with_edited_transcript

(Graveley et al., 2011)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-13

Cytogenetic map

64C7-64C7

Sequence location

3L:5,141,953..5,144,317 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

64C7-64C7

Limits computationally determined from genome sequence between P{PZ}l(3)rG166^rG166 and P{PZ}sinu⁰⁶⁵²⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-13

(FlyBase, 2016)

3-12.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

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

Bloomington

93820

y¹ w^*; TI{CRIMIC.TG4.0}Gdap1^{CR70263-TG4.0}

76554

y¹ sc^* v¹ sev²¹; P{TKO.GS01005}attP40

79692

y¹ sc^* v¹ sev²¹; P{TOE.GS01416}attP40

51903

y¹ sc^* v¹ sev²¹; P{TRiP.HMC03477}attP40

NIG-Fly

4623R-1

P{NIG.4623R}1

HMJ23188

y¹ v¹; P{TRiP.HMJ23188}attP40/CyO

VDRC

v106485

P{KK108177}VIE-260B

v21624

w¹¹¹⁸; P{GD10713}v21624

Genomic Clones (7)

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

cDNA Clones (280)

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

RE69232

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.

FBgn0035587

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0035587

Antibody Information

Laboratory Generated Antibodies

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: Gdap1 CG4623

(López Del Amo et al., 2015)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (6)

Reported As

Name Synonyms

GDAP1 ortholog

Gdap1

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 ( 43 )

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.

38597

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.

Q9VRJ3

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.

Q9VRJ3

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0035587

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

38597/tissue=All

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

FBgn0035587

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

FBgn0035587

FlyMine - An integrated database for Drosophila genomics

FBgn0035587

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

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

dme:Dmel_CG4623

MARRVEL_MODEL - MARRVEL (model organism gene)

38597

Linkouts

BioGRID - A database of protein and genetic interactions.

64065

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

FBgn0035587

DroID - A comprehensive database of gene and protein interactions.

FBgn0035587

DRSC - Results frm RNAi screens

FBgn0035587

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

CG4623_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0035587

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0035587

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

CG4623

Flygut - An atlas of the Drosophila adult midgut

FBgn0035587

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

FBgn0035587

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

TC003336

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

38597

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class I peroxisomal membrane protein import

References (48)

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

0.14

Report Sections