FlyBase Gene Report: Dmel\prage

General Information

Symbol

Dmel\prage

Species

D. melanogaster

Name

prage

Annotation Symbol

CG42666

Feature Type

protein_coding_gene

FlyBase ID

FBgn0283741

Gene Model Status

Current

Stock Availability

21 publicly available

Gene Summary

prage (prage) encodes a protein involved in maternal mRNA destabilization during the maternal/zygotic transition in embryonic development. [Date last reviewed: 2019-03-28] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

EG:131F2.2 , prg, EG:137E7.1

Key Links

Genomic Location

Cytogenetic map

2B9-2B12

Sequence location

X:1,773,719..1,853,667 [+]

Recombination map

1-0.2

RefSeq locus

NC_004354 REGION:1773719..1853667

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 (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables exonuclease activity

inferred from biological aspect of ancestor with PANTHER:PTN000300925

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR047021

(InterPro Project Members, 2004-)

enables nucleic acid binding

inferred from electronic annotation with InterPro:IPR036397

(InterPro Project Members, 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in egg activation

inferred from mutant phenotype

(Tadros et al., 2003)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in rRNA 3'-end processing

inferred from biological aspect of ancestor with PANTHER:PTN000301072

(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 nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000300925

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

UNCLASSIFIED NUCLEASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

prage (prage) encodes a protein involved in maternal mRNA destabilization during the maternal/zygotic transition in embryonic development. [Date last reviewed: 2019-03-28]

Gene Group (FlyBase)

UNCLASSIFIED NUCLEASES -: This group comprises nucleases that do not classify under other groups in FlyBase.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\prage 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 C7LAE5)

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 5.55

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

Gene model reviewed during 5.41

Shares 5' UTR with upstream gene (one isoform only).

Gene model reviewed during 5.46

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

prage-RA

FBtr0302657

NM_166906

2876

761

prage-RB

FBtr0302654

NM_130589

3467

787

prage-RC

FBtr0302656

NM_166907

3100

761

prage-RD

FBtr0302655

NM_166908

2934

742

prage-RE

FBtr0302658

NM_001201599

3629

852

prage-RF

FBtr0302659

NM_001201600

3806

761

prage-RG

FBtr0309966

NM_001258549

3319

742

prage-RH

FBtr0309967

NM_001258550

2784

742

prage-RI

FBtr0309968

NM_001258551

2821

742

prage-RJ

FBtr0309969

NM_001258552

3749

852

prage-RK

FBtr0332901

NM_001272214

3700

742

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

prage-PA

FBpp0291797

84.3

761

7.77

FBpp0291794

87.0

787

7.74

FBpp0291796

84.3

761

7.77

FBpp0291795

82.0

742

7.85

FBpp0291798

94.4

852

8.34

FBpp0291799

84.3

761

7.77

FBpp0301693

82.0

742

7.85

FBpp0301694

82.0

742

7.85

FBpp0301695

82.0

742

7.85

FBpp0301696

94.4

852

8.34

FBpp0305122

82.0

742

7.85

Q8IRW9

NP_001259143

AGB94989

Polypeptides with Identical Sequences

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

742 aa isoforms: prage-PD, prage-PG, prage-PH, prage-PI, prage-PK

761 aa isoforms: prage-PA, prage-PC, prage-PF

852 aa isoforms: prage-PE, prage-PJ

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\prage 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).

3.70

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

anlage in statu nascendi

(Fisher et al., 2012)

dorsal ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)

organism | ubiquitous

• cytoplasm | basal

Comment: apically cleared

(Fisher et al., 2012)

yolk

(Fisher et al., 2012)

yolk nucleus

(Fisher et al., 2012)

embryonic stage 7 -- 8

amnioserosa anlage

(Fisher et al., 2012)

dorsal ectoderm

(Fisher et al., 2012)

yolk nucleus

(Fisher et al., 2012)

embryonic stage 9 -- 10

amnioserosa

(Fisher et al., 2012)

amnioserosa primordium

(Fisher et al., 2012)

dorsal ectoderm

(Fisher et al., 2012)

yolk nucleus

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

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\prage in JBrowse

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

View exonic expression by developmental stage for Dmel\prage

View exonic expression by tissue for Dmel\prage

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

FBgn0261548

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

31136/tissue=All

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

FBgn0283741

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

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

FBgn0283741

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 23 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of prage

Transgenic constructs containing regulatory region of prage

Aberrations (Deficiencies and Duplications) ( 9 )

Inferred from experimentation ( 9 )

Gene disrupted in

Df(1)BSC719

(Cui et al., 2016)

Df(1)tR15

(Tadros et al., 2003)

T(1;3)sc^J4

(Tadros et al., 2003)

Gene not disrupted in

Df(1)260-1

(Cui et al., 2016, Tadros et al., 2003)

Df(1)A94

(Cui et al., 2016, Tadros et al., 2003)

(Cui et al., 2016)

(Cui et al., 2016)

(Cui et al., 2016)

(Tadros et al., 2003)

Inferred from location ( 29 )

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, with Scer\GAL4^Mef2.PR

prage^GD8446

lethal | pupal stage, with Scer\GAL4^pnr-MD237

prage^GD8446

lethal - all die during P-stage, with Scer\GAL4^Mef2.PR

prage^GD3195

partially lethal - majority die, with Scer\GAL4^pnr-MD237

prage^GD3195

partially lethal - majority die | pupal stage, with Scer\GAL4^pnr-MD237

prage^GD8446

viable

prage^d10828

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

viable, with Scer\GAL4^tin.CΔ4

prage^GD8446

Sterility

Allele

fertile

prage^d10828

Other Phenotypes

Allele

some die during pupal stage, with Scer\GAL4^pnr-MD237

prage^GD3195

visible, with Scer\GAL4^pnr-MD237

Phenotype manifest in

Allele

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

prage^GD3195

mesonotum, with Scer\GAL4^pnr-MD237

trichogen cell, with Scer\GAL4^pnr-MD237

prage^GD8446

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) (9)

Hsap\REXO1

6 of 14

Yes

5 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

1 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) (10)

Rnor\Rexo1l1-ps1

6 of 14

Yes

Rnor\Rexo1

6 of 14

Yes

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

1 of 14

Yes

Rnor\Isg20

1 of 14

Rnor\Trex1

1 of 14

Mus musculus (laboratory mouse) (10)

Mmus\Rexo1

6 of 14

Yes

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Yes

Mmus\Trex1

1 of 14

Mmus\Trex2

1 of 14

Xenopus tropicalis (Western clawed frog) (8)

Xtro\wdr53

4 of 13

Yes

3 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Danio rerio (Zebrafish) (6)

Drer\rexo1

7 of 14

Yes

6 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (5)

Cele\Y56A3A.33

8 of 14

Yes

7 of 14

3 of 14

2 of 14

2 of 14

Anopheles gambiae (African malaria mosquito) (7)

Agam\AgaP_AGAP003847

6 of 12

Yes

3 of 12

2 of 12

2 of 12

2 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (10)

Atha\AT5G25800

6 of 13

Yes

Atha\SDN1

4 of 13

Yes

Atha\SDN2

4 of 13

Yes

Atha\SDN3

4 of 13

Yes

Atha\AT2G48100

2 of 13

Yes

Atha\AT3G15080

2 of 13

Atha\AT3G27970

2 of 13

Yes

Atha\AT3G50090

2 of 13

Yes

Atha\AT5G40310

2 of 13

Yes

Atha\DPD1

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (4)

Scer\REX3

7 of 13

Yes

Scer\RNH70

5 of 13

Scer\PAN2

2 of 13

Scer\REX4

2 of 13

Schizosaccharomyces pombe (Fission yeast) (4)

Spom\rex3

7 of 12

Yes

Spom\SPAC637.09

4 of 12

Spom\SPBC1604.09c

2 of 12

Spom\ubp13

2 of 12

Escherichia coli (enterobacterium) (5)

Ecol\cas2

1 of 11

Yes

Ecol\dnaQ

1 of 11

Yes

Ecol\exoX

1 of 11

Yes

Ecol\recE

1 of 11

Yes

Ecol\rnt

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:prage. 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)

9 of 13

4 of 13

4 of 13

2 of 13

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 ( 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?

REXO1; RNA exonuclease 1 homolog

6 of 14

609614

REXO1L1P; REXO1 like 1, pseudogene

5 of 14

AEN; apoptosis enhancing nuclease

3 of 14

610177

ISG20L2; interferon stimulated exonuclease gene 20 like 2

3 of 14

611930

REXO5; RNA exonuclease 5

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

esyN Network Diagram

Other Interaction Browsers

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Ribosome biogenesis in eukaryotes

Class of Gene

gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-0.2

Cytogenetic map

2B9-2B12

Sequence location

X:1,773,719..1,853,667 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

2B9-2B12

; Limits computationally determined from genome sequence between P{EP}br^EP1515 and P{EP}EP1444&P{EP}CG14818^EP1190

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-0.2

(FlyBase, 2016, Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (21)

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

Bloomington

603879

P{SX4.lexA::HG}prage^S24-14A w¹¹¹⁸

41050

y¹ Mi{MIC}prage^MI04620 w^*

41535

y¹ Mi{MIC}prage^MI06875 w^*

43698

y¹ Mi{MIC}prage^MI07282 w^*

11126

11263

11299

11312

v103667

v38826

w¹¹¹⁸; P{GD8446}v38826

v38827

w¹¹¹⁸; P{GD8446}v38827

v6921

w¹¹¹⁸; P{GD3195}v6921/CyO

More stocks available...

Genomic Clones (52)

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

cDNA Clones (70)

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

IP20073

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.

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R⁺ cells.

(Boutros et al., 2004)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG14799 CG14801

(FlyBase Genome Annotators, 2010)

Source for merge of: CG14800 EG:131F2.2

(FlyBase, 1996-)

Source for merge of: EG:131F2.2 EG:137E7.1

(FlyBase Genome Annotators, 2002-2003)

Source for merge of: prage CG42666

(Cui et al., 2016)

Additional comments

Annotations CG14799 and CG14801 merged as CG42666 in release 5.25 of the genome annotation.

(FlyBase Genome Annotators, 2010)

Annotations CG14801, CG14800 and CG17968 merged as CG14801 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Source for merge of CG14800 EG:131F2.2 was a shared EST (SD04906) ( date:010919 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

The gene is named "prage", the Sanskrit word for "early", as mutant embryos show defects in the early syncytial stages.

(Tadros et al., 2003)

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG14799

(Keleman et al., 2009.8.5, Lin and Kellis, 2006.12.15)

CG14800

(Boutros et al., 2004, Benos, 2000.12.13)

CG14801

(Álvarez-Fernández et al., 2015, Chandran et al., 2014, Smibert et al., 2012)

CG17968

(Mount, 2001.8.14, Benos, 2000.12.13)

CG42666

(Khoroshko et al., 2020, Gerstberger et al., 2017, Cui et al., 2016, Hosono et al., 2015, Chen et al., 2014, Fukuoh et al., 2014, Chen et al., 2013, Han et al., 2011, FlyBase Genome Annotators, 2010, Ni et al., 2010.12.1)

EG:131F2.2

(Kim et al., 2005)

EG:137E7.1

(Benos et al., 2001)

REXO1

(Gerstberger et al., 2017)

prage

(Khoroshko et al., 2020, Meltzer et al., 2019, Gene Disruption Project members, 2016-)

prg

(Cui et al., 2016, Tadros et al., 2003)

Name Synonyms

prage

(Cui et al., 2016, Sackton et al., 2007, Tadros et al., 2003)

Secondary FlyBase IDs

FBgn0067662
FBgn0261548
FBgn0024988
FBgn0029591
FBgn0023543
FBgn0029592

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 86 )

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.

31136

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.

C7LAE5

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.

C7LAE5

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0261548

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

31136/tissue=All

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

FBgn0283741

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

FBgn0283741

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

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

dme:Dmel_CG42666

MARRVEL_MODEL - MARRVEL (model organism gene)

31136

Linkouts

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0283741

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

TC034835

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Ribosome biogenesis in eukaryotes

References (60)

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

3.70

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