FlyBase Gene Report: Dmel\mus304

FB2024_03 , released June 25, 2024

FB2024_03 , released June 25, 2024

Gene: Dmel\mus304

General Information

Symbol

Dmel\mus304

Species

D. melanogaster

Name

mutagen-sensitive 304

Annotation Symbol

CG7347

Feature Type

protein_coding_gene

FlyBase ID

FBgn0002901

Gene Model Status

Stock Availability

8 publicly available

Gene Summary

DNA damage checkpoint protein required for chromosome break repair and for genomic stability during development. (UniProt, Q9VVN4)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
UniProtKB
Red Book
Interactive Fly

Also Known As

ATRIP, mus-304, ATR-interacting protein

Key Links

Genomic Location

Cytogenetic map

Sequence location

3L:18,109,814..18,112,847 [+]

Recombination map

3-45

RefSeq locus

NT_037436 REGION:18109814..18112847

Sequence

Get Decorated FASTA

Genomic Maps

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (11 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (10 terms)

Terms Based on Experimental Evidence (8 terms)

CV Term

Evidence

References

involved_in DNA damage checkpoint signaling

inferred from mutant phenotype

(Brodsky et al., 2000)

involved_in DNA repair

inferred from mutant phenotype

(Brodsky et al., 2000)

involved_in female meiosis chromosome segregation

inferred from mutant phenotype

(Brodsky et al., 2000)

involved_in female meiotic nuclear division

inferred from mutant phenotype

(Brodsky et al., 2000)

involved_in mitotic DNA replication checkpoint signaling

inferred from mutant phenotype

(Lee et al., 2012)

involved_in reciprocal meiotic recombination

inferred from mutant phenotype

(Brodsky et al., 2000)

involved_in regulation of syncytial blastoderm mitotic cell cycle

inferred from mutant phenotype

(Brodsky et al., 2000)

involved_in telomere maintenance

inferred from genetic interaction with FLYBASE:tefu; FB:FBgn0045035

(Bi et al., 2005)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in DNA damage checkpoint signaling

inferred from electronic annotation with InterPro:IPR033349

(InterPro Project Members, 2004-)

involved_in DNA repair

inferred from biological aspect of ancestor with PANTHER:PTN002408403

(GO Reference Genome Project, 2011-)

involved_in imaginal disc development

traceable author statement

(Walworth, 2000)

involved_in response to radiation

traceable author statement

(Walworth, 2000)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Brodsky et al., 2000)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the ATRIP family. (Q9VVN4)

Protein Signatures (InterPro)

ATR-interacting protein

Summaries

Protein Function (UniProtKB)

DNA damage checkpoint protein required for chromosome break repair and for genomic stability during development.

(UniProt, Q9VVN4)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

mus304 (J.B. Boyd)

Larval survival hypersensitive to exposure to methyl methanesulfonate and nitrogen mustard. Neither hypermutable to alkylating agents nor defective in alkylation repair pathway; however, defective in UV-damage repair pathway (Smith and Dusenberg, 1988, Mechanisms and Consequences of DNA Damage Processing, Alan R. Liss, Inc., pp. 251-55). When fertile, homozygous females exhibit uniformly decreased recombination along the X chromosome (Green, 1982, Biol. Zentralbl. 101: 223-26). Partially deficient in post-replication repair (Boyd and Shaw, 1982, Mol. Gen. Genet. 186: 289-94) and excision (Boyd and Harris, 1981, Chromosoma 97: 607-23); DNA synthesis modified (Boyd and Shaw).

Gene Model and Products

Number of Transcripts

1

Number of Unique Polypeptides

1

Please see the JBrowse view of Dmel\mus304 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 Q9VVN4)

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 5.46

Sequence Ontology: Class of Gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FBtr0075122

2816

846

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

FBpp0074888

96.1

846

6.55

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)

Interacts with ATR/mei-41.

(UniProt, Q9VVN4)

Domain

The EEXXXDDL motif is required for the interaction with ATR/mei-41.

(UniProt, Q9VVN4)

Crossreferences

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

ATR-interacting protein

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\mus304 using the Feature Mapper tool.

External Data

Crossreferences

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

mus304_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).

0.66

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

Comment: maternally deposited

(Fisher et al., 2012)

embryonic cycle 1 -- embryonic cycle 13

organism | ubiquitous | uniform

(Brodsky et al., 2000)

adult stage | female oogenesis stage S5 -- S14

(Brodsky et al., 2000)

(Brodsky et al., 2000)

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

(Brodsky et al., 2000)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\mus304 in JBrowse

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

View exonic expression by developmental stage for Dmel\mus304

View exonic expression by tissue for Dmel\mus304

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

FBgn0002901

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

40003/tissue=All

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

FBgn0002901

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0002901

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

FBgn0002901

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

CG7347

Flygut - An atlas of the Drosophila adult midgut

FBgn0002901

Images

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 ( 6 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of mus304

Transgenic constructs containing regulatory region of mus304

Aberrations (Deficiencies and Duplications) ( 3 )

Inferred from experimentation ( 3 )

Gene disrupted in

(Ryder, 2004.4.26)

(Brodsky et al., 2000)

(Brodsky et al., 2000)

Inferred from location ( 0 )

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

mus304^GD4217

viable, with Scer\GAL4^Mef2.PR

mus304^GD4217

viable, with Scer\GAL4^pnr-MD237

mus304^GD4217

Other Phenotypes

Allele

abnormal DNA repair

abnormal meiotic cell cycle | recessive

abnormal mitotic cell cycle | recessive

mus304^unspecified

abnormal neuroanatomy | larval stage | conditional, with Scer\GAL4^19-12

abnormal neuroanatomy | larval stage | conditional, with Scer\GAL4^elav.PU

mus304^HMJ23247

chemical sensitive

chemical sensitive (with Df(3L)W4)

mus304^D1

chemical sensitive | recessive

increased cell death

mus304^unspecified

radiation sensitive | recessive

mus304^D1

visible, with Scer\GAL4^pnr-MD237

mus304^GD4217

visible | recessive

mus304^Tag:FLAG

Phenotype manifest in

Allele

axon | larval stage | conditional, with Scer\GAL4^19-12

axon | larval stage | conditional, with Scer\GAL4^elav.PU

mus304^HMJ23247

chromosome (with mus304^D1)

mus304^D3

chromosome (with mus304^D3)

mus304^D1

embryo | embryonic cycle 13

mus304^unspecified

larval multidendritic class III neuron | conditional, with Scer\GAL4^19-12

larval multidendritic class III neuron | conditional, with Scer\GAL4^elav.PU

mus304^HMJ23247

mesothoracic tergum, with Scer\GAL4^pnr-MD237

mus304^GD4217

mitosis & nuclear chromosome

mus304^unspecified

mitotic cell cycle

mus304^unspecified

mitotic domain 1 | embryonic cycle 12

mus304^unspecified

mitotic domain 1 | embryonic cycle 14

mus304^unspecified

nucleus | embryonic stage

mus304^unspecified

mus304^unspecified

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) (1)

1 of 14

Yes

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) (1)

1 of 14

Yes

Yes

Mus musculus (laboratory mouse) (1)

1 of 14

Yes

Yes

Xenopus tropicalis (Western clawed frog) (1)

1 of 13

Yes

Yes

Danio rerio (Zebrafish) (1)

1 of 14

Yes

Yes

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP008194

8 of 12

Yes

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:mus304. 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?

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

esyN Network Diagram

Other Interaction Browsers

Summary of Genetic Interactions

esyN Network Diagram

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

esyN Network Key:

Suppression

Enhancement

Other 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

(Oikemus et al., 2006)

enhanceable

(Brodsky et al., 2000)

enhanceable

(Oikemus et al., 2006)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(Bi et al., 2005)

enhanceable

(Oikemus et al., 2006)

enhanceable

(Oikemus et al., 2006, Bi et al., 2005)

External Data

Subunit Structure (UniProtKB)

Interacts with ATR/mei-41.

(UniProt, Q9VVN4 )

Linkouts

BioGRID - A database of protein and genetic interactions.

65288

DroID - A comprehensive database of gene and protein interactions.

FBgn0002901

MIST (genetic) - An integrated Molecular Interaction Database

40003

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

3L

Recombination map

3-45

Cytogenetic map

Sequence location

3L:18,109,814..18,112,847 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

75B9-75B10

Limits computationally determined from genome sequence between P{lacW}l(3)j11B2^j11B2 and P{PZ}W⁰⁵⁰¹⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

75B-75B

(Brodsky, 2000.1.13)

Experimentally Determined Recombination Data

Location

3-45

(FlyBase, 2016)

3-41.6

(Comeron et al., 2012)

3-

(Boyd et al., 1981)

3-46

Left of (cM)

cu

(Boyd et al., 1981)

Right of (cM)

st

(Boyd et al., 1981)

Notes

Stocks and Reagents

Stocks (8)

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

923

61355

y¹ v¹; P{TRiP.HMJ23247}attP40

922

st¹ mus304^D1/TM3, Sb¹ Ser¹

106127

106126

st¹ mus304^D1/TM3, Sb¹ Ser¹

HMJ23247

y¹ v¹; P{TRiP.HMJ23247}attP40/CyO

v46012

w¹¹¹⁸ P{GD4217}v46012

v46011

w¹¹¹⁸; P{GD4217}v46011/TM3

Genomic Clones (29)

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

cDNA Clones (55)

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

LD44887

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.

FBgn0002901

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0002901

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

mus304 is essential for cell cycle arrest at high doses of X-irradiation.

(Oikemus et al., 2006)

mus304 is required for a functional DNA damage checkpoint in the developing eye.

(Brodsky et al., 2000)

Gene is involved in post-replication recombination repair.

(de Buendia, 1998)

Larval survival hypersensitive to exposure to methyl methanesulfonate and nitrogen mustard. Neither hypermutable to alkylating agents nor defective in alkylation repair pathway; however, defective in UV-damage repair pathway (Smith and Dusenbery, 1988). When fertile, homozygous females exhibit uniformly decreased recombination along the X chromosome (Green, 1982). Partially deficient in post-replication repair (Boyd and Shaw, 1982) and excision (Boyd and Harris, 1981); DNA synthesis modified (Boyd and Shaw, 1982).

Relationship to Other Genes

Source for database merge of

Source for merge of: mus304 CG7347

(Millburn, 2000.4.17)

Source for merge of: mus304 anon-WO0140519.82

(FlyBase, 1996-)

Additional comments

Source for merge of mus304 anon-WO0140519.82 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (11)

Reported As

Symbol Synonym

ATRIP

(Kizhedathu et al., 2021, Amaral et al., 2017, Raffa et al., 2013, Kondo and Perrimon, 2011, Cenci et al., 2008, Rong, 2008)

CG7347

(Perkins et al., 2009, Millburn, 2000.4.17)

Mus304

(Siddiqui et al., 2012, Hochwagen, 2006)

anon-WO0140519.82

atrip

(Morciano et al., 2009, Oikemus et al., 2006)

mus(3)304

(The Moscow Regional Drosophila melanogaster Stock Center, Dubna)

mus-304

(Raffa et al., 2013, Walworth, 2000)

Name Synonyms

ATR-interacting protein

(Raffa et al., 2013, Rong, 2008)

mutagen sensitive 304

(Morciano et al., 2009)

mutagen-sensitive 304

(Davis et al., 2011, Mukai et al., 2006)

Secondary FlyBase IDs

FBgn0036776
FBgn0044544

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 37 )

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.

40003

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.

Q9VVN4

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

Q9VVN4

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.

Q9VVN4

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0002901

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

40003/tissue=All

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

FBgn0002901

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

FBgn0002901

FlyMine - An integrated database for Drosophila genomics

FBgn0002901

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

ATR-interacting protein

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

dme:Dmel_CG7347

MARRVEL_MODEL - MARRVEL (model organism gene)

40003

Linkouts

BioGRID - A database of protein and genetic interactions.

65288

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

FBgn0002901

DroID - A comprehensive database of gene and protein interactions.

FBgn0002901

DRSC - Results frm RNAi screens

FBgn0002901

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

mus304_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0002901

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0002901

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

CG7347

Flygut - An atlas of the Drosophila adult midgut

FBgn0002901

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

FBgn0002901

MIST (genetic) - An integrated Molecular Interaction Database

40003

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

References (79)