FlyBase Gene Report: Dmel\axed

General Information

Symbol

Dmel\axed

Species

D. melanogaster

Name

axundead

Annotation Symbol

CG8398

Feature Type

protein_coding_gene

FlyBase ID

FBgn0035708

Gene Model Status

Current

Stock Availability

12 publicly available

Gene Summary

BACK (BTB and C-terminal Kelch) domain protein - a mediator of axon death - axed mutants suppress axon death - acts in glia downstream of sarm - pro-degenerative pathways activated by Sarm signaling or Nmnat elimination ultimately converge on Axed - possibly involved in recruitment of substrates to Cullin Ring Ubiquitin Ligase complexes B (Interactive Fly, axed )

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

65C1-65C1

Sequence location

3L:6,609,325..6,619,113 [+]

Recombination map

3-17

RefSeq locus

NT_037436 REGION:6609325..6619113

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 neurogenesis

inferred from biological aspect of ancestor with PANTHER:PTN001229949

(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 cytosol

inferred from biological aspect of ancestor with PANTHER:PTN001229949

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Summary (Interactive Fly)

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\axed 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 A0A4D6K4X9)

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 5.44

Gene model reviewed during 5.46

Stop-codon suppression (UGA) postulated; FBrf0216884, FBrf0234051.

Gene model reviewed during 6.25

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

axed-RA

FBtr0076978

NM_139794

2878

537

axed-RC

FBtr0076980

NM_168174

1850

435

axed-RD

FBtr0076981

NM_206283

2094

435

axed-RE

FBtr0330184

NM_168173

1911

435

axed-RF

FBtr0474136

NM_001370050

2878

582

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

axed-PA

FBpp0076687

61.1

537

7.29

FBpp0076689

49.3

435

7.35

FBpp0076690

49.3

435

7.35

FBpp0303217

49.3

435

7.35

FBpp0423135

65.9

582

5.53

QCD26218

Polypeptides with Identical Sequences

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

435 aa isoforms: axed-PC, axed-PD, axed-PE

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

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\axed using the Feature Mapper tool.

External Data

Crossreferences

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

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).

3.84

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11 -- 12

yolk nucleus

(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

Reporter: Mi{PT-GFSTF.1}axed^{MI13270-GFSTF.1}

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

larval ventral nerve cord

(Neukomm et al., 2017)

adult stage

neuron of adult brain

(Neukomm et al., 2017)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\axed in JBrowse

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

View exonic expression by developmental stage for Dmel\axed

View exonic expression by tissue for Dmel\axed

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

FBgn0035708

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

38741/tissue=All

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

FBgn0035708

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0035708

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

FBgn0035708

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

CG8398

Flygut - An atlas of the Drosophila adult midgut

FBgn0035708

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\axed

Stages(s) 11-12

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 13 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 11 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of axed

Transgenic constructs containing regulatory region of axed

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 4 )

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 | recessive

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

axed^GD13915

viable, with Scer\GAL4^Mef2.PR

axed^GD13915

viable, with Scer\GAL4^pnr-MD237

axed^GD13915

Other Phenotypes

Allele

abnormal neuroanatomy | adult stage, with Scer\GAL4^455.2

axed^UAS.long

abnormal neuroanatomy | adult stage | conditional, with Spyo\Cas9^ey.3x211

axed^U6:3.gRNA

abnormal stress response, with Spyo\Cas9^ey.3x211

axed^U6:3.gRNA

abnormal stress response | larval stage, with Scer\GAL4^21-7

axed^HMJ22228

abnormal stress response | larval stage, with Spyo\Cas9^SOP.scE1x8

axed^U6:3.gRNA

abnormal wound healing | adult stage

axed²⁰⁹⁴

abnormal wound healing | adult stage | somatic clone

Phenotype manifest in

Allele

adult mechanosensory neuron, with Scer\GAL4^455.2

axed^UAS.long

adult olfactory receptor neuron Or22 | conditional, with Spyo\Cas9^ey.3x211

axed^U6:3.gRNA

axon | adult stage

axed²⁰⁹⁴

axon | adult stage, with Scer\GAL4^455.2

axed^UAS.long

axon | adult stage | conditional, with Spyo\Cas9^ey.3x211

axed^U6:3.gRNA

axon | adult stage | somatic clone

axon | larval stage, with Scer\GAL4^21-7

axed^HMJ22228

axon | larval stage, with Spyo\Cas9^SOP.scE1x8

axed^U6:3.gRNA

dendrite | larval stage, with Spyo\Cas9^SOP.scE1x8

axed^U6:3.gRNA

larval dorsal multidendritic neuron ddaC, with Scer\GAL4^21-7

axed^HMJ22228

larval dorsal multidendritic neuron ddaC, with Spyo\Cas9^SOP.scE1x8

axed^U6:3.gRNA

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) (6)

Hsap\BTBD6

3 of 14

Yes

2 of 14

2 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) (6)

Rnor\Btbd1

2 of 14

Yes

Rnor\Btbd3

2 of 14

Yes

Rnor\Btbd6

2 of 14

Yes

Rnor\Btbd2

1 of 14

Rnor\Btbd17

1 of 14

Rnor\Btbd19

1 of 14

Mus musculus (laboratory mouse) (6)

Mmus\Btbd6

3 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (4)

Xtro\ifngr1

2 of 13

Yes

Xtro\atp10d

1 of 13

Xtro\btbd3

1 of 13

Xtro\btbd6

1 of 13

Danio rerio (Zebrafish) (6)

Drer\btbd6a

3 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (4)

Cele\F47B10.9

1 of 14

Yes

Cele\F56C3.9

1 of 14

Yes

Cele\tag-30

1 of 14

Yes

Cele\W07A12.4

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (4)

Agam\AgaP_AGAP005408

10 of 12

Yes

Agam\AgaP_AGAP004234

2 of 12

Agam\AgaP_AGAP000791

1 of 12

Agam\AgaP_AGAP013431

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:axed. 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) (5)

3 of 13

2 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Wallerian degeneration

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?

BTBD6; BTB domain containing 6

3 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

protein-protein

Physical Interaction

Assay

References

axed - Wnk

anti bait coimmunoprecipitation, anti tag western blot

(Izadifar et al., 2021)

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

enhanceable

(Ji et al., 2022)

suppressible

(Izadifar et al., 2021)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(Ji et al., 2022)

suppressible

(Neukomm et al., 2017)

Nmnat

suppressible

Sarm|axed

(Neukomm et al., 2017)

Sarm

suppressible

axed

(Neukomm et al., 2017)

Wnk

suppressible

axed

(Izadifar et al., 2021)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

64191

DroID - A comprehensive database of gene and protein interactions.

FBgn0035708

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene_with_stop_codon_read_through

(Jungreis et al., 2016, Jungreis, 2011.11.18)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-17

Cytogenetic map

65C1-65C1

Sequence location

3L:6,609,325..6,619,113 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

65C1-65C1

Limits computationally determined from genome sequence between P{PZ}l(3)02094⁰²⁰⁹⁴ and P{lacW}l(3)L4060^L4060

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-17

(FlyBase, 2016)

3-15.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (12)

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

Bloomington

606768

w^*; PBac{U6:3-axed.gRNA}VK00027

20994

w¹¹¹⁸; P{GT1}axed^GT-000966

58220

y¹ v¹; P{TRiP.HMJ22228}attP40

62928

y¹ v¹; P{TRiP.HMJ30005}attP40

51106

y¹ w^*; Mi{MIC}axed^MI08716

54510

y¹ w^*; Mi{MIC}axed^MI10175

65070

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06003}attP40

58041

y¹ w^*; Mi{MIC}axed^MI13270/TM3, Sb¹ Ser¹

NIG-Fly

HMJ22228

y¹ v¹; P{TRiP.HMJ22228}attP40/CyO

HMJ30005

y¹ v¹; P{TRiP.HMJ30005}attP40/CyO

VDRC

v35927

w¹¹¹⁸; P{GD13915}v35927

v35928

w¹¹¹⁸; P{GD13915}v35928/TM3

Genomic Clones (26)

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

cDNA Clones (33)

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

AT21853

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.

FBgn0035708

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0035708

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

Source for merge of: CG8398 anon- EST:Posey31

(Bayraktaroglu, 2000.11.2)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: axed CG8398

(Neukomm et al., 2017)

Nomenclature comments

Etymology

The gene is named 'axundead' based on the phenotype of long-term survival of severed axons that should otherwise undergo axon death.

(Neukomm et al., 2017)

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

Axed

(Coleman and Höke, 2020, Neukomm et al., 2018.1.29)

CG8398

(Neukomm et al., 2017, Jungreis et al., 2016, Aradska et al., 2015, Jungreis, 2011.11.18, Jungreis et al., 2011, Shapira et al., 2011, Ni et al., 2010.12.1, Perkins et al., 2009)

anon-EST:Posey31

axed

(Ji et al., 2022, Llobet Rosell et al., 2022, Majane et al., 2022, Hsu et al., 2021, Izadifar et al., 2021, Rosell and Neukomm, 2019, Sapar and Han, 2019, Neukomm et al., 2017)

Name Synonyms

axundead

(Majane et al., 2022, Farley et al., 2018, Neukomm et al., 2017)

Secondary FlyBase IDs

FBgn0027687

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.

38741

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.

A0A4D6K4X9

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.

A0A4D6K4X9

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0035708

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

38741/tissue=All

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

FBgn0035708

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

FBgn0035708

FlyMine - An integrated database for Drosophila genomics

FBgn0035708

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

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

dme:Dmel_CG8398

MARRVEL_MODEL - MARRVEL (model organism gene)

38741

Linkouts

BioGRID - A database of protein and genetic interactions.

64191

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

FBgn0035708

DroID - A comprehensive database of gene and protein interactions.

FBgn0035708

DRSC - Results frm RNAi screens

FBgn0035708

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0035708

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0035708

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

CG8398

Flygut - An atlas of the Drosophila adult midgut

FBgn0035708

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

FBgn0035708

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

TC003028

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

Interactive Fly

References (36)

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

3.84

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