FlyBase Gene Report: Dmel\pcm

General Information

Symbol

Dmel\pcm

Species

D. melanogaster

Name

pacman

Annotation Symbol

CG3291

Feature Type

protein_coding_gene

FlyBase ID

FBgn0020261

Gene Model Status

Stock Availability

5 publicly available

Gene Summary

pacman (pcm) encodes an exoribonuclease that degrades decapped mRNA. It is involved in epithelial closure, male fertility, apoptosis and growth control. [Date last reviewed: 2019-09-26] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

XRN1, dXRN1

Key Links

Genomic Location

Cytogenetic map

Sequence location

X:19,485,759..19,492,011 [-]

Recombination map

1-62

RefSeq locus

NC_004354 REGION:19485759..19492011

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (24 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 5'-3' exoribonuclease activity

inferred from biological aspect of ancestor with PANTHER:PTN002643517

(assigned by GO_Central )

(Gaudet et al., 2011)

enables RNA binding

inferred from biological aspect of ancestor with PANTHER:PTN002643517

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (16 terms)

Terms Based on Experimental Evidence (14 terms)

CV Term

Evidence

References

involved_in dorsal closure

inferred from mutant phenotype

(Grima et al., 2008)

involved_in imaginal disc fusion, thorax closure

inferred from mutant phenotype

(Grima et al., 2008)

involved_in imaginal disc-derived wing morphogenesis

inferred from mutant phenotype

(Grima et al., 2008)

involved_in mRNA catabolic process

inferred from direct assay

(Nishioka et al., 2018)

involved_in negative regulation of apoptotic process

inferred from mutant phenotype

(Waldron et al., 2015)

involved_in negative regulation of gene expression

inferred from genetic interaction with FLYBASE:Psc; FB:FBgn0005624

(Nishioka et al., 2018)

involved_in nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3'

inferred from mutant phenotype

(Bönisch et al., 2007)

involved_in nuclear-transcribed mRNA catabolic process, non-stop decay

inferred from mutant phenotype

(Kashima et al., 2014)

inferred from genetic interaction with FLYBASE:pix; FB:FBgn0086706

(Kashima et al., 2014)

involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

inferred from mutant phenotype

(Rehwinkel et al., 2005)

involved_in positive regulation of imaginal disc growth

inferred from mutant phenotype

(Waldron et al., 2015)

involved_in regulation of cytoplasmic mRNA processing body assembly

inferred from mutant phenotype

(Lin et al., 2008)

involved_in RNA interference

inferred from mutant phenotype

(Rehwinkel et al., 2005)

involved_in spermatogenesis

inferred from mutant phenotype

(Zabolotskaya et al., 2008)

involved_in wound healing

inferred from mutant phenotype

(Grima et al., 2008)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in nuclear-transcribed mRNA catabolic process

inferred from biological aspect of ancestor with PANTHER:PTN002643517

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in rRNA catabolic process

inferred from biological aspect of ancestor with PANTHER:PTN004352441

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (6 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Lin et al., 2008)

part_of messenger ribonucleoprotein complex

inferred from direct assay

(assigned by UniProt )

(Barbee et al., 2006)

located_in neuronal cell body

inferred from direct assay

(assigned by UniProt )

(Hillebrand et al., 2010)

located_in neuronal ribonucleoprotein granule

inferred from direct assay

(assigned by UniProt )

(Hillebrand et al., 2010, Barbee et al., 2006)

located_in P-body

inferred from direct assay

(Zabolotskaya et al., 2008)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN002643517

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

5'-3'-EXORIBONUCLEASES

Protein Family (UniProt)

-

Protein Signatures (InterPro)

Summaries

Gene Snapshot

pacman (pcm) encodes an exoribonuclease that degrades decapped mRNA. It is involved in epithelial closure, male fertility, apoptosis and growth control. [Date last reviewed: 2019-09-26]

Gene Group (FlyBase)

5'-3'-EXORIBONUCLEASES -: 5'-3'-exoribonucleases catalyze the sequential degradation of mononucleotides from a free 5' terminus of an RNA molecule.

Summary (Interactive Fly)

exoribonuclease that degrades decapped mRNA - directly interacts with Decapping protein 1 to couple mRNA decapping to 5' exonucleolytic degradation - required for degradation of mRNAs targeted by NMD and RNAi - regulates polycomb silencing - regulates insulin-like peptide and the neuropeptide-like precursor Nplp2 mRNA levels - affects apoptosis and regulates expression of and - regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in wing imaginal discs

Interactive Fly

Gene Model and Products

Number of Transcripts

2

Number of Unique Polypeptides

2

Please see the JBrowse view of Dmel\pcm 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

Comments on Gene Model

Gene model reviewed during 5.45

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FBtr0074784

5260

1612

FBtr0302082

5384

1613

Additional Transcript Data and Comments

Reported size (kB)

5.2 (northern blot)

(Till et al., 1998)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

FBpp0074553

184.5

1612

7.03

FBpp0291292

184.6

1613

7.03

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

1613 (aa)

(Till et al., 1998)

Comments

External Data

Crossreferences

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

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\pcm using the Feature Mapper tool.

External Data

Crossreferences

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

pcm_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 2 -- 10

organism | ubiquitous

(Till et al., 1998)

embryonic stage 6 -- 10

(Till et al., 1998)

(Till et al., 1998)

embryonic stage 13 -- 17

organism | faint | ubiquitous

(Till et al., 1998)

adult stage | female & oogenesis stage S3

(Till et al., 1998)

adult stage | female oogenesis stage S3 -- S10

(Till et al., 1998)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 7

organism | ubiquitous

(Till et al., 1998)

embryonic stage 1 -- 12

Comment: reference states 0-8 hr AEL

(Till et al., 1998)

adult stage | female

(Till et al., 1998)

adult stage | male

(Till et al., 1998)

adult stage & oogenesis

(Till et al., 1998)

(Till et al., 1998)

Additional Descriptive Data

pcm transcripts are abundantly expressed in 0-4 and 4-8hr embryos and in adult males and females. pcm transcripts are first detected by in situ hybridization in stage 3 egg chambers in both nurse cells and the oocyte. By stage 10, expression is mainly in nurse cells with very little expression in the oocyte. In embryos, transcripts are ubiquitously distributed and are particularly abundant in the germ band and in head structures.

(Till et al., 1998)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

germinal proliferation center

(Zabolotskaya et al., 2008)

adult stage | male & spermatogenesis

• P-body

(Zabolotskaya et al., 2008)

primary spermatocyte

• P-body

(Zabolotskaya et al., 2008)

oogenesis stage S2 -- S7

Comment: in discrete foci

(Lin et al., 2008)

oogenesis stage S2 -- S9

Comment: concentrated at posterior end

(Lin et al., 2008)

oogenesis stage S9

Comment: ubiquitous

(Lin et al., 2008)

Additional Descriptive Data

pcm protein is localized to the apical end of the testis, and to cytoplasmic foci in spermatogonia and primary spermatocytes. pcm is colocalized with DCP1 and me31B protein in the cytoplasmic foci.

(Zabolotskaya et al., 2008)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Lin et al., 2008)

part_of messenger ribonucleoprotein complex

inferred from direct assay

(assigned by UniProt )

(Barbee et al., 2006)

located_in neuronal cell body

inferred from direct assay

(assigned by UniProt )

(Hillebrand et al., 2010)

located_in neuronal ribonucleoprotein granule

inferred from direct assay

(assigned by UniProt )

(Hillebrand et al., 2010, Barbee et al., 2006)

located_in P-body

inferred from direct assay

(Zabolotskaya et al., 2008)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\pcm in GBrowse 2

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

View exonic expression by developmental stage for Dmel\pcm

View exonic expression by tissue for Dmel\pcm

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

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0020261

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG3291-RA

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

CG3291

Flygut - An atlas of the Drosophila adult midgut

FBgn0020261

Images

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 9 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 10 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of pcm

Transgenic constructs containing regulatory region of pcm

Aberrations (Deficiencies and Duplications) ( 4 )

Inferred from experimentation ( 4 )

Gene disrupted in

(Ryder, 2004.4.26)

(Lin et al., 2008)

Gene partially disrupted in

(Waldron et al., 2015)

(Waldron et al., 2015)

Inferred from location ( 0 )

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal - all die during P-stage

pcm¹⁵

lethal - all die during pupal stage

pcm¹⁴

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

pcm^GD10926

partially lethal - majority live | cold sensitive (with Df(1)JA27)

pcm⁵

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

pcm^GD10926

viable, with Scer\GAL4^tin.CΔ4

pcm^GD10926

Sterility

Allele

female semi-sterile | recessive

Other Phenotypes

Allele

abnormal developmental rate

pcm¹⁴

abnormal developmental rate | larval stage

pcm¹⁴

abnormal developmental rate | third instar larval stage

pcm¹⁵

abnormal flight, with Scer\GAL4^Mef2.PR

pcm^GD10926

abnormal pain response | adult stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

pcm^GD10926

abnormal size | adult stage

pcm⁵

abnormal size | third instar larval stage

pcm¹⁴

abnormal size | third instar larval stage, with Scer\GAL4^69B

pcm^GD10926

abnormal size | third instar larval stage, with Scer\GAL4^nub-AC-62

pcm^GD10926

abnormal wound healing

increased cell death, with Scer\GAL4^69B

pcm^GD10926

increased cell death, with Scer\GAL4^en.PU

pcm^GD10926

increased cell death, with Scer\GAL4^nub-AC-62

pcm^GD10926

increased cell death | third instar larval stage

increased occurrence of cell division | third instar larval stage

pcm¹⁴

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

pcm^GD10926

visible, with Scer\GAL4^69B

pcm^GD10926

visible, with Scer\GAL4^en.PU

pcm^GD10926

visible, with Scer\GAL4^nub-AC-62

pcm^GD10926

visible, with Scer\GAL4^pnr-MD237

pcm^GD10926

visible (with Df(1)JA27)

pcm⁵

visible | cold sensitive

pcm⁵

Phenotype manifest in

Allele

egg chamber | oogenesis stage S9

embryonic/first instar larval cuticle (with Df(1)JA27)

pcm⁵

eye disc | third instar larval stage

pcm¹⁴

haltere disc | third instar larval stage

pcm¹⁴

mesothoracic tergum, with Scer\GAL4^pnr-MD237

pcm^GD10926

metathoracic femur | cold sensitive

pcm⁵

metathoracic leg disc | third instar larval stage

pcm¹⁴

P-body | cold sensitive

pcm⁵

P-body | cold sensitive (with Df(1)JA27)

pcm⁵

posterior wing margin, with Scer\GAL4^en.PU

pcm^GD10926

posterior wing margin | cold sensitive

pcm⁵

pupal thorax | cold sensitive (with Df(1)JA27)

pcm⁵

pcm⁵

wing (with Df(1)JA27)

pcm⁵

wing | cold sensitive

pcm⁵

wing blade, with Scer\GAL4^69B

pcm^GD10926

wing blade, with Scer\GAL4^en.PU

pcm^GD10926

wing blade, with Scer\GAL4^nub-AC-62

pcm^GD10926

wing disc | third instar larval stage

wing pouch, with Scer\GAL4^69B

pcm^GD10926

wing pouch, with Scer\GAL4^en.PU

pcm^GD10926

wing pouch, with Scer\GAL4^nub-AC-62

pcm^GD10926

wing vein, with Scer\GAL4^69B

pcm^GD10926

wing vein, with Scer\GAL4^en.PU

pcm^GD10926

wing vein, with Scer\GAL4^nub-AC-62

pcm^GD10926

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

12 of 15

Yes

Yes

2

3 of 15

No

No

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

12 of 15

Yes

Yes

2 of 15

No

No

Rattus norvegicus (Norway rat) (3)

11 of 13

Yes

Yes

3 of 13

No

No

Rnor\LOC100911537

2 of 13

No

Yes

Xenopus tropicalis (Western clawed frog) (2)

8 of 12

Yes

Yes

2 of 12

No

No

Danio rerio (Zebrafish) (2)

11 of 15

Yes

Yes

3 of 15

No

No

Caenorhabditis elegans (Nematode, roundworm) (2)

12 of 15

Yes

Yes

3 of 15

No

No

Arabidopsis thaliana (thale-cress) (3)

4 of 9

Yes

No

4 of 9

Yes

No

3 of 9

No

No

Saccharomyces cerevisiae (Brewer's yeast) (2)

10 of 15

Yes

Yes

5 of 15

No

No

Schizosaccharomyces pombe (Fission yeast) (2)

10 of 12

Yes

Yes

2 of 12

No

No

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091900LL )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Dsuz\DS10_00004775

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Drosophila persimilis

Drosophila willistoni

Drosophila virilis

Drosophila mojavensis

Drosophila grimshawi

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500D4 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Glossina morsitans

Tsetse fly

Gmor\GMOY007142

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_02325

Mayetiola destructor

Hessian fly

Mdes\Mdes002069

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL008814

Anopheles darlingi

American malaria mosquito

Adar\ADAC000711

Anopheles gambiae

Malaria mosquito

Agam\AGAP004430

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ007753

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00TE )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA000473

Danaus plexippus

Monarch butterfly

Dple\DPOGS205725-PA

Danaus plexippus

Monarch butterfly

Dple\DPOGS210043-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL005907

Apis florea

Little honeybee

Aflo\2360505588

Apis mellifera

Western honey bee

Bombus impatiens

Common eastern bumble bee

Bombus terrestris

Buff-tailed bumblebee

Linepithema humile

Argentine ant

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:000f84

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG000119

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG003470

Dendroctonus ponderosae

Mountain pine beetle

Tribolium castaneum

Red flour beetle

Pediculus humanus

Human body louse

Phum\PHUM577340

Rhodnius prolixus

Kissing bug

Rpro\RPRC002660

Cimex lectularius

Bed bug

Clec\CLEC008458

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI084157

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI004449

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_01744

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00S5 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR014375

Ixodes scapularis

Black-legged tick

Isca\ISCW019569

Stegodyphus mimosarum

African social velvet spider

Smim\KFM72723.1

Stegodyphus mimosarum

African social velvet spider

Smim\KFM72724.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur25g00400

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G00A4 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_007729gn

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000025127

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000022336

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000001334

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (1)

Gene Symbol

Score

Source

Alignment

5 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

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 v8.0 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?

XRN1; 5'-3' exoribonuclease 1

12 of 15

XRN2; 5'-3' exoribonuclease 2

3 of 15

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

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

nuclear magnetic resonance, predetermined participant, anti tag coimmunoprecipitation, anti tag western blot, anti bait coimmunoprecipitation, western blot, pull down, molecular weight estimation by staining

(Braun et al., 2012)

anti tag coimmunoprecipitation, anti tag western blot

(Braun et al., 2012)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

pull down, western blot

(Antic et al., 2015)

RNA-protein

Physical Interaction

Assay

References

ribonuclease assay, molecular weight estimation by staining

(Nishioka et al., 2018)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

(Waldron et al., 2015)

suppressible

(Waldron et al., 2015)

suppressible

(Towler et al., 2016)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

(Waldron et al., 2015)

suppressible

(Waldron et al., 2015)

suppressible

(Nishioka et al., 2018)

enhanceable

(Nishioka et al., 2018)

suppressible

(Nishioka et al., 2018)

enhanceable

(Nishioka et al., 2018)

enhanceable

(Nishioka et al., 2018)

suppressible

(Nishioka et al., 2018)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

59237

DroID - A comprehensive database of gene and protein interactions.

FBgn0020261

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

32935

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

pcm

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

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

Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA

Genomic Location and Detailed Mapping Data

Chromosome (arm)

X

Recombination map

1-62

Cytogenetic map

Sequence location

X:19,485,759..19,492,011 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

18C7-18C7

Limits computationally determined from genome sequence between P{EP}EP1526&P{EP}Pfrx^EP1150 and P{EP}Tao-1^EP1455

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

18C1-18C4

(Newbury et al., 1998, Newbury and Till, 1997)

Experimentally Determined Recombination Data

Location

1-62

(FlyBase, 2016)

1-61.6

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

33263

w^* P{EP}pcm^G1726

34690

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01169}attP2

44442

y¹ sc^* v¹ sev²¹; P{TRiP.GLC01410}attP40

v105739

P{KK108511}VIE-260B

v21677

w¹¹¹⁸; P{GD10926}v21677

Genomic Clones (13)

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

cDNA Clones (32)

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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

LD22664

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.

FBgn0020261

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0020261

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

32935

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Grima et al., 2008, Zabolotskaya et al., 2008)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: pcm CG3291

(Benos, 1999.11)

Source for database merge of

Additional comments

Other Comments

Changes in expression profiles associated with the unfolded protein response have been analyzed in S2 cells following treatment with dsRNA made from templates generated with primers directed against this gene.

(Hollien and Weissman, 2006)

dsRNA has been made from templates generated with primers directed against this gene.

(Rehwinkel et al., 2005)

The pcm product is required for the degradation of 3' decay intermediates.

(Rehwinkel et al., 2005)

Origin and Etymology

Discoverer

Etymology

Identification

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.

32935

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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

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

FBgn0020261

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

pcm_1

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

CG3291

Flygut - An atlas of the Drosophila adult midgut

FBgn0020261

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

32935

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

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

Dmel_CG3291

modMine - A data warehouse for the modENCODE project

FBgn0020261

Linkouts

BioGRID - A database of protein and genetic interactions.

59237

DroID - A comprehensive database of gene and protein interactions.

FBgn0020261

DRSC - Results frm RNAi screens

FBgn0020261

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0020261

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG3291-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0020261

FlyMine - An integrated database for Drosophila genomics

FBgn0020261

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

Interactive Fly

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

32935

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

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

pcm

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

Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

CG3291

(Çiçek et al., 2016, Hosono et al., 2015, Ding et al., 2014, Kashima et al., 2014, Han et al., 2011, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Hollien and Weissman, 2006, Labourier et al., 2002)

DmXrn1

(Jinek et al., 2011)

Pcm

(Nishioka et al., 2018, Hillebrand et al., 2010, Kuan et al., 2009)

XRN1

(Temme et al., 2014, Nagarajan et al., 2013, Nishihara et al., 2013, Braun et al., 2012, Han et al., 2011, Lindquist et al., 2011, Haas et al., 2010, Behm-Ansmant et al., 2007, Eulalio et al., 2007, Rehwinkel et al., 2005, Rehwinkel et al., 2005, Valencia-Sanchez and Maquat, 2004)

XRN1/pcm

(Hollien and Weissman, 2006)

Xrn1

(Waldron et al., 2015, Kashima et al., 2014, Bönisch et al., 2007)

Xrn1p

(Valencia-Sanchez et al., 2006)

dXRN1

(Dai et al., 2020, Wu et al., 2019)

Name Synonyms

PACMAN

(Nagarajan et al., 2013)

Pacman

(Eichler et al., 2020, Han et al., 2011, Lin et al., 2008, Zabolotskaya et al., 2008, Barbee et al., 2006, Zaessinger et al., 2006, Rehwinkel et al., 2005, Morgan, 2002)

pacman

(Towler et al., 2016, Handler et al., 2013, Lim et al., 2009, Grima et al., 2008, Lin et al., 2008, Schneider et al., 2006, Newbury, 1999.5.25, Newbury and Till, 1997)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (90)