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Gene 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	Current	Stock availability	4 publicly available
Also Known As	XRN1
Genomic Location
Chromosome (arm)	X	Recombination map
Cytogenetic map	18C7-18C7	Sequence location	X:19,379,913..19,385,984 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene pacman is referred to in FlyBase by the symbol Dmel\pcm (CG3291, FBgn0020261). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: 5'-3' exoribonuclease activity. There is experimental evidence that it is involved in the biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; dorsal closure; RNA interference; regulation of cytoplasmic mRNA processing body assembly; wound healing; imaginal disc fusion, thorax closure; nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3'; imaginal disc-derived wing morphogenesis; spermatogenesis. 12 alleles are reported. The phenotypes of these alleles are annotated with: embryonic/first instar larval cuticle; testis; mesothoracic tergum; wing; spermatozoon. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: 5'-3' exoribonuclease 1; Putative 5-3 exonuclease. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval/adult central nervous system, larval midgut, larval hindgut, larval Malpighian tubules, larval/adult fat body, larval salivary gland, larval trachea, adult female reproductive system, adult male reproductive system, larval carcass. Comments on Affy2 ProbeSet: ProbeSet 1624778_at partially aligns to an exonic region common to each of the 2 FlyBase-annotated transcript isoforms of pcm: 11 out of 13 probes fall into this exonic region. Gene sequence location is X:19379913..19385984.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2011_10
FB2012_01	Sequence features HFA20361 BKN28511
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 18C7-18C7   Limits computationally determined from genome sequence between P{EP}EP1526&P{EP}PfrxEP1150 and P{EP}Tao-1EP1455
Experimentally Determined Cytological Location
Cytogenetic map Notes References 18C1-18C4     (Newbury et al., 1998) 18C1-18C4     (Newbury and Till, 1997)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\pcm for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) pcm-RA FBtr0074784  NM_078684   5200   1612 pcm-RB FBtr0302082  NM_001169325   5203   1613
Additional Transcript Data & 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 protein pcm-PA   FBpp0074553   184.5   1612   7.03     NP_523408   AAF48958 pcm-PB   FBpp0291292   184.6   1613   7.03     NP_001162796   ACZ95330
Additional Polypeptide Data & Comments
Reported size (kDa)	1613 (aa) (Till et al., 1998)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Putative 5-3 exonuclease (IPR004859) 5'-3' exoribonuclease 1 (IPR016494)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA263439   AA695377   AA817398   AA820637   AA820728   AA942280   AA949784   AE014298 AAF48958   AE014298 ACZ95330   AI061920   AI134050   AI512305   AI516353   AI531870   AI945245   AJ242529 CAB43711   AW942649   AY051675 AAK93099   BF486421   BF488539   BF493587   BF501867   BF503215   BG638473   BG639602   CK660988   CO280278   CO282122   CO293802   CO325716   CO328077   EC062057   EC212680   EC235441   EC252880   EC255547   EV595162   EV598748
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9VWI1 Q9XZU2 E1JJR3
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
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   germ band   (Till et al., 1998) embryonic head   (Till et al., 1998) embryonic stage 13 -- 17   organism | faint & ubiquitous   (Till et al., 1998) adult stage | female & oogenesis stage S3   oocyte   (Till et al., 1998) adult stage | femaleoogenesis stage S3 -- S10   nurse cell   (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     (Till et al., 1998) Comment:reference states 0-8 hr AEL adult stage | female     (Till et al., 1998) adult stage | male     (Till et al., 1998) adult stage & oogenesis   oocyte   (Till et al., 1998) nurse cell   (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
Notes
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. modENCODE Temporal Expression Data for FBgn0020261    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0020261 Very low expression bin max Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages. [download data (TSV)] Guide to modENCODE expression level colors   No expression (0 - 0)   Extremely low expression (1 - 10)   Very low expression (11 - 100)   Low expression (101 - 400)   Moderate expression (401 - 1400)   Moderately high expression (1401 - 4000)   High expression (4001 - 10000)   Very high expression (10001 - 100000)   Extremely high expression (100001 - 2000000) Linear, scaled to maximum FBgn0020261 expression level Developmental Stage   Expression Level embryo 00-02hr    4213 embryo 02-04hr    2380 embryo 04-06hr    1900 embryo 06-08hr    2254 embryo 08-10hr    1885 embryo 10-12hr    1575 embryo 12-14hr    1145 embryo 14-16hr    1399 embryo 16-18hr    868 embryo 18-20hr    650 embryo 20-22hr    708 embryo 22-24hr    567 larva L1    1222 larva L2    791 larva L3 12hr old    691 larva L3 puffstage 1-2    665 larva L3 puffstage 3-6    1124 larva L3 puffstage 7-9    1242 white prepupae new    1332 white prepupae 12hr    1183 white prepupae 24hr    1577 pupae 2d postWPP    1047 pupae 3d postWPP    674 pupae 4d postWPP    816 adult male 01day    1030 adult male 05day    1278 adult male 30day    1343 adult female 01day    1746 adult female 05day    2141 adult female 30day    2166 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (4213) embryo 02-04hr  (2380) embryo 04-06hr  (1900) embryo 06-08hr  (2254) embryo 08-10hr  (1885) embryo 10-12hr  (1575) embryo 12-14hr  (1145) embryo 14-16hr  (1399) embryo 16-18hr  (868) embryo 18-20hr  (650) embryo 20-22hr  (708) embryo 22-24hr  (567) larva L1  (1222) larva L2  (791) larva L3 12hr old  (691) larva L3 puffstage 1-2  (665) larva L3 puffstage 3-6  (1124) larva L3 puffstage 7-9  (1242) white prepupae new  (1332) white prepupae 12hr  (1183) white prepupae 24hr  (1577) pupae 2d postWPP  (1047) pupae 3d postWPP  (674) pupae 4d postWPP  (816) adult male 01day  (1030) adult male 05day  (1278) adult male 30day  (1343) adult female 01day  (1746) adult female 05day  (2141) adult female 30day  (2166) Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (4213) embryo 02-04hr  (2380) embryo 04-06hr  (1900) embryo 06-08hr  (2254) embryo 08-10hr  (1885) embryo 10-12hr  (1575) embryo 12-14hr    1145 embryo 14-16hr    1399 embryo 16-18hr    868 embryo 18-20hr    650 embryo 20-22hr    708 embryo 22-24hr    567 larva L1    1222 larva L2    791 larva L3 12hr old    691 larva L3 puffstage 1-2    665 larva L3 puffstage 3-6    1124 larva L3 puffstage 7-9    1242 white prepupae new    1332 white prepupae 12hr    1183 white prepupae 24hr  (1577) pupae 2d postWPP    1047 pupae 3d postWPP    674 pupae 4d postWPP    816 adult male 01day    1030 adult male 05day    1278 adult male 30day    1343 adult female 01day  (1746) adult female 05day  (2141) adult female 30day  (2166) Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    4213 embryo 02-04hr    2380 embryo 04-06hr    1900 embryo 06-08hr    2254 embryo 08-10hr    1885 embryo 10-12hr    1575 embryo 12-14hr    1145 embryo 14-16hr    1399 embryo 16-18hr    868 embryo 18-20hr    650 embryo 20-22hr    708 embryo 22-24hr    567 larva L1    1222 larva L2    791 larva L3 12hr old    691 larva L3 puffstage 1-2    665 larva L3 puffstage 3-6    1124 larva L3 puffstage 7-9    1242 white prepupae new    1332 white prepupae 12hr    1183 white prepupae 24hr    1577 pupae 2d postWPP    1047 pupae 3d postWPP    674 pupae 4d postWPP    816 adult male 01day    1030 adult male 05day    1278 adult male 30day    1343 adult female 01day    1746 adult female 05day    2141 adult female 30day    2166 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    4213 embryo 02-04hr    2380 embryo 04-06hr    1900 embryo 06-08hr    2254 embryo 08-10hr    1885 embryo 10-12hr    1575 embryo 12-14hr    1145 embryo 14-16hr    1399 embryo 16-18hr    868 embryo 18-20hr    650 embryo 20-22hr    708 embryo 22-24hr    567 larva L1    1222 larva L2    791 larva L3 12hr old    691 larva L3 puffstage 1-2    665 larva L3 puffstage 3-6    1124 larva L3 puffstage 7-9    1242 white prepupae new    1332 white prepupae 12hr    1183 white prepupae 24hr    1577 pupae 2d postWPP    1047 pupae 3d postWPP    674 pupae 4d postWPP    816 adult male 01day    1030 adult male 05day    1278 adult male 30day    1343 adult female 01day    1746 adult female 05day    2141 adult female 30day    2166 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0020261 expression level Developmental Stage   Expression Level embryo 00-02hr    4213 embryo 02-04hr    2380 embryo 04-06hr    1900 embryo 06-08hr    2254 embryo 08-10hr    1885 embryo 10-12hr    1575 embryo 12-14hr    1145 embryo 14-16hr    1399 embryo 16-18hr    868 embryo 18-20hr    650 embryo 20-22hr    708 embryo 22-24hr    567 larva L1    1222 larva L2    791 larva L3 12hr old    691 larva L3 puffstage 1-2    665 larva L3 puffstage 3-6    1124 larva L3 puffstage 7-9    1242 white prepupae new    1332 white prepupae 12hr    1183 white prepupae 24hr    1577 pupae 2d postWPP    1047 pupae 3d postWPP    674 pupae 4d postWPP    816 adult male 01day    1030 adult male 05day    1278 adult male 30day    1343 adult female 01day    1746 adult female 05day    2141 adult female 30day    2166 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High  log, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (4213) embryo 02-04hr  (2380) embryo 04-06hr  (1900) embryo 06-08hr  (2254) embryo 08-10hr  (1885) embryo 10-12hr  (1575) embryo 12-14hr  (1145) embryo 14-16hr  (1399) embryo 16-18hr  (868) embryo 18-20hr  (650) embryo 20-22hr  (708) embryo 22-24hr  (567) larva L1  (1222) larva L2  (791) larva L3 12hr old  (691) larva L3 puffstage 1-2  (665) larva L3 puffstage 3-6  (1124) larva L3 puffstage 7-9  (1242) white prepupae new  (1332) white prepupae 12hr  (1183) white prepupae 24hr  (1577) pupae 2d postWPP  (1047) pupae 3d postWPP  (674) pupae 4d postWPP  (816) adult male 01day  (1030) adult male 05day  (1278) adult male 30day  (1343) adult female 01day  (1746) adult female 05day  (2141) adult female 30day  (2166) Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (4213) embryo 02-04hr  2380 embryo 04-06hr  1900 embryo 06-08hr  2254 embryo 08-10hr  1885 embryo 10-12hr  1575 embryo 12-14hr    1145 embryo 14-16hr    1399 embryo 16-18hr    868 embryo 18-20hr    650 embryo 20-22hr    708 embryo 22-24hr    567 larva L1    1222 larva L2    791 larva L3 12hr old    691 larva L3 puffstage 1-2    665 larva L3 puffstage 3-6    1124 larva L3 puffstage 7-9    1242 white prepupae new    1332 white prepupae 12hr    1183 white prepupae 24hr  1577 pupae 2d postWPP    1047 pupae 3d postWPP    674 pupae 4d postWPP    816 adult male 01day    1030 adult male 05day    1278 adult male 30day    1343 adult female 01day  1746 adult female 05day  2141 adult female 30day  2166 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    4213 embryo 02-04hr    2380 embryo 04-06hr    1900 embryo 06-08hr    2254 embryo 08-10hr    1885 embryo 10-12hr    1575 embryo 12-14hr    1145 embryo 14-16hr    1399 embryo 16-18hr    868 embryo 18-20hr    650 embryo 20-22hr    708 embryo 22-24hr    567 larva L1    1222 larva L2    791 larva L3 12hr old    691 larva L3 puffstage 1-2    665 larva L3 puffstage 3-6    1124 larva L3 puffstage 7-9    1242 white prepupae new    1332 white prepupae 12hr    1183 white prepupae 24hr    1577 pupae 2d postWPP    1047 pupae 3d postWPP    674 pupae 4d postWPP    816 adult male 01day    1030 adult male 05day    1278 adult male 30day    1343 adult female 01day    1746 adult female 05day    2141 adult female 30day    2166 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    4213 embryo 02-04hr    2380 embryo 04-06hr    1900 embryo 06-08hr    2254 embryo 08-10hr    1885 embryo 10-12hr    1575 embryo 12-14hr    1145 embryo 14-16hr    1399 embryo 16-18hr    868 embryo 18-20hr    650 embryo 20-22hr    708 embryo 22-24hr    567 larva L1    1222 larva L2    791 larva L3 12hr old    691 larva L3 puffstage 1-2    665 larva L3 puffstage 3-6    1124 larva L3 puffstage 7-9    1242 white prepupae new    1332 white prepupae 12hr    1183 white prepupae 24hr    1577 pupae 2d postWPP    1047 pupae 3d postWPP    674 pupae 4d postWPP    816 adult male 01day    1030 adult male 05day    1278 adult male 30day    1343 adult female 01day    1746 adult female 05day    2141 adult female 30day    2166 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     FlyAtlas Anatomical Expression Data for FBgn0020261    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0020261 Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval/adult central nervous system, larval midgut, larval hindgut, larval Malpighian tubules, larval/adult fat body, larval salivary gland, larval trachea, adult female reproductive system, adult male reproductive system, larval carcass. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (1000 - 25000) Linear, scaled to maximum FBgn0020261 expression level Tissue   Expression Level Larval Central Nervous System    337.125 Larval Midgut    105.2 Larval Hindgut    137.4 Larval Malpighian Tubules    118.1 Larval Fat Body    151.1 Larval Salivary Gland    195.4 Larval Trachea    155.7 Larval Carcass    189.025 Adult Head    84.2 Adult Eye    65.1 Adult Brain    186.9 Adult Thoracic-Abdominal Ganglion    117.9 Adult Crop    79.5 Adult Midgut    84.4 Adult Hindgut    71.3 Adult Malpighian Tubules    99.3 Adult Fat Body    111.1 Adult Salivary Gland    99.2 Adult Heart    62.35 Adult VirginFemale Spermatheca    87.3 Adult InseminatedFemale Spermatheca    104.8 Adult Ovary    345.3 Adult Testis    214.3 Adult Male Accessory Gland    102.4 Adult Carcass    82.3 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    337.125 Larval Midgut    105.2 Larval Hindgut    137.4 Larval Malpighian Tubules    118.1 Larval Fat Body    151.1 Larval Salivary Gland    195.4 Larval Trachea    155.7 Larval Carcass    189.025 Adult Head    84.2 Adult Eye    65.1 Adult Brain    186.9 Adult Thoracic-Abdominal Ganglion    117.9 Adult Crop    79.5 Adult Midgut    84.4 Adult Hindgut    71.3 Adult Malpighian Tubules    99.3 Adult Fat Body    111.1 Adult Salivary Gland    99.2 Adult Heart    62.35 Adult VirginFemale Spermatheca    87.3 Adult InseminatedFemale Spermatheca    104.8 Adult Ovary    345.3 Adult Testis    214.3 Adult Male Accessory Gland    102.4 Adult Carcass    82.3 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    337.125 Larval Midgut    105.2 Larval Hindgut    137.4 Larval Malpighian Tubules    118.1 Larval Fat Body    151.1 Larval Salivary Gland    195.4 Larval Trachea    155.7 Larval Carcass    189.025 Adult Head    84.2 Adult Eye    65.1 Adult Brain    186.9 Adult Thoracic-Abdominal Ganglion    117.9 Adult Crop    79.5 Adult Midgut    84.4 Adult Hindgut    71.3 Adult Malpighian Tubules    99.3 Adult Fat Body    111.1 Adult Salivary Gland    99.2 Adult Heart    62.35 Adult VirginFemale Spermatheca    87.3 Adult InseminatedFemale Spermatheca    104.8 Adult Ovary    345.3 Adult Testis    214.3 Adult Male Accessory Gland    102.4 Adult Carcass    82.3 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    337.125 Larval Midgut    105.2 Larval Hindgut    137.4 Larval Malpighian Tubules    118.1 Larval Fat Body    151.1 Larval Salivary Gland    195.4 Larval Trachea    155.7 Larval Carcass    189.025 Adult Head    84.2 Adult Eye    65.1 Adult Brain    186.9 Adult Thoracic-Abdominal Ganglion    117.9 Adult Crop    79.5 Adult Midgut    84.4 Adult Hindgut    71.3 Adult Malpighian Tubules    99.3 Adult Fat Body    111.1 Adult Salivary Gland    99.2 Adult Heart    62.35 Adult VirginFemale Spermatheca    87.3 Adult InseminatedFemale Spermatheca    104.8 Adult Ovary    345.3 Adult Testis    214.3 Adult Male Accessory Gland    102.4 Adult Carcass    82.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0020261 expression level Tissue   Expression Level Larval Central Nervous System    337.125 Larval Midgut    105.2 Larval Hindgut    137.4 Larval Malpighian Tubules    118.1 Larval Fat Body    151.1 Larval Salivary Gland    195.4 Larval Trachea    155.7 Larval Carcass    189.025 Adult Head    84.2 Adult Eye    65.1 Adult Brain    186.9 Adult Thoracic-Abdominal Ganglion    117.9 Adult Crop    79.5 Adult Midgut    84.4 Adult Hindgut    71.3 Adult Malpighian Tubules    99.3 Adult Fat Body    111.1 Adult Salivary Gland    99.2 Adult Heart    62.35 Adult VirginFemale Spermatheca    87.3 Adult InseminatedFemale Spermatheca    104.8 Adult Ovary    345.3 Adult Testis    214.3 Adult Male Accessory Gland    102.4 Adult Carcass    82.3 Expression Level Scale  None   Low   Moderate   High  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    337.125 Larval Midgut    105.2 Larval Hindgut    137.4 Larval Malpighian Tubules    118.1 Larval Fat Body    151.1 Larval Salivary Gland    195.4 Larval Trachea    155.7 Larval Carcass    189.025 Adult Head    84.2 Adult Eye    65.1 Adult Brain    186.9 Adult Thoracic-Abdominal Ganglion    117.9 Adult Crop    79.5 Adult Midgut    84.4 Adult Hindgut    71.3 Adult Malpighian Tubules    99.3 Adult Fat Body    111.1 Adult Salivary Gland    99.2 Adult Heart    62.35 Adult VirginFemale Spermatheca    87.3 Adult InseminatedFemale Spermatheca    104.8 Adult Ovary    345.3 Adult Testis    214.3 Adult Male Accessory Gland    102.4 Adult Carcass    82.3 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    337.125 Larval Midgut    105.2 Larval Hindgut    137.4 Larval Malpighian Tubules    118.1 Larval Fat Body    151.1 Larval Salivary Gland    195.4 Larval Trachea    155.7 Larval Carcass    189.025 Adult Head    84.2 Adult Eye    65.1 Adult Brain    186.9 Adult Thoracic-Abdominal Ganglion    117.9 Adult Crop    79.5 Adult Midgut    84.4 Adult Hindgut    71.3 Adult Malpighian Tubules    99.3 Adult Fat Body    111.1 Adult Salivary Gland    99.2 Adult Heart    62.35 Adult VirginFemale Spermatheca    87.3 Adult InseminatedFemale Spermatheca    104.8 Adult Ovary    345.3 Adult Testis    214.3 Adult Male Accessory Gland    102.4 Adult Carcass    82.3 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    337.125 Larval Midgut    105.2 Larval Hindgut    137.4 Larval Malpighian Tubules    118.1 Larval Fat Body    151.1 Larval Salivary Gland    195.4 Larval Trachea    155.7 Larval Carcass    189.025 Adult Head    84.2 Adult Eye    65.1 Adult Brain    186.9 Adult Thoracic-Abdominal Ganglion    117.9 Adult Crop    79.5 Adult Midgut    84.4 Adult Hindgut    71.3 Adult Malpighian Tubules    99.3 Adult Fat Body    111.1 Adult Salivary Gland    99.2 Adult Heart    62.35 Adult VirginFemale Spermatheca    87.3 Adult InseminatedFemale Spermatheca    104.8 Adult Ovary    345.3 Adult Testis    214.3 Adult Male Accessory Gland    102.4 Adult Carcass    82.3 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    84.2   NA  Eye    65.1   NA  Brain    186.9   337.125  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    117.9   NA  Crop    79.5   105.2  Midgut    84.4   137.4  Hindgut    71.3   118.1  Malpighian Tubules    99.3   151.1  Fat Body    111.1   195.4  Salivary Gland    99.2   NA  Heart    62.35   155.7  Trachea    NA   NA  VirginFemale Spermatheca    87.3   NA  InseminatedFemale Spermatheca    104.8   NA  Ovary    345.3   NA  Testis    214.3   NA  Male Accessory Gland    102.4   189.025  Carcass    82.3 modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010) mE2_34_mRNA_expression_cluster_06
External Data & 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
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele semi-lethal | pupal stage, with Scer\GAL4pnr-MD237 pcmGD10926 semi-viable | cold sensitive (with Df(1)JA27) pcm5 viable pcm2 pcm3 pcm5 pcm6 pcmhs.PG Sterility Allele female semi-sterile | recessive pcm3 pcm5 fertile | reduced pcm3 pcm5 Other Phenotypes Allele visible, with Scer\GAL4pnr-MD237 pcmGD10926 visible (with Df(1)JA27) pcm5 visible | cold sensitive pcm5 wound healing defective pcm3 pcm5 Phenotype manifest in Allele cytoplasmic mRNA processing body | cold sensitive pcm5 cytoplasmic mRNA processing body | cold sensitive (with Df(1)JA27) pcm5 egg chamber | oogenesis stage S9 pcm3 pcm5 embryonic/first instar larval cuticle (with Df(1)JA27) pcm5 mesothoracic tergum, with Scer\GAL4pnr-MD237 pcmGD10926 metathoracic femur | cold sensitive pcm5 posterior wing margin | cold sensitive pcm5 pupal thorax | cold sensitive (with Df(1)JA27) pcm5 spermatozoon pcm3 pcm5 testis pcm3 pcm5 wing (with Df(1)JA27) pcm5 wing | cold sensitive pcm5
Classical Alleles ( 6 )
For All Classical Alleles Show
Allele of pcm Class Mutagen Stocks Known lesion pcmG1726 P-element activity 1 -- pcm5 amorphic allele - molecular evidence P-element activity 0 Yes pcm2 P-element activity 0 Yes pcm3 hypomorphic allele - molecular evidence P-element activity 0 Yes pcm6 P-element activity 0 Yes pcmΔ1 P-element activity 0 --
Alleles Carried on Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Allele of pcm Class Mutagen Stocks Known lesion pcmGD10926 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes pcmHMS01169 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes pcmKK108511 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes pcmAct5C.T:Disc\RFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes pcmhs.PG in vitro construct - regulatory fusion 0 Yes pcmN.Scer\UAS.T:Avic\GFP in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(1)Exel7468 (Ryder, 2004.4.26) Df(1)JA27 (Lin et al., 2008)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD10926} NA P{KK108511} NA P{TRiP.HMS01169} NA P{UAS-pcm.GFP.N} NA heat-shock construct P{hs-pcm.G} NA characterization construct P{Act5C-pcm-RFP} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EP}EP1526 NA P{EP}pcmG1726 NA
Gene Ontology: Function, Process & Cellular Component ( 15 unique terms )
Terms Based on Experimental Evidence ( 12 terms )
Molecular Function
CV term Evidence References
5'-3' exoribonuclease activity inferred from direct assay (Newbury et al., 2000)
Biological Process
CV term Evidence References
dorsal closure inferred from mutant phenotype (Grima et al., 2008) imaginal disc-derived wing morphogenesis inferred from mutant phenotype (Grima et al., 2008) imaginal disc fusion, thorax closure inferred from mutant phenotype (Grima et al., 2008) nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' inferred from mutant phenotype (Bönisch et al., 2007) nuclear-transcribed mRNA catabolic process, nonsense-mediated decay inferred from mutant phenotype (Rehwinkel et al., 2005) regulation of cytoplasmic mRNA processing body assembly inferred from mutant phenotype (Lin et al., 2008) RNA interference inferred from mutant phenotype (Rehwinkel et al., 2005) spermatogenesis inferred from mutant phenotype (Zabolotskaya et al., 2008) wound healing inferred from mutant phenotype (Grima et al., 2008)
Cellular Component
CV term Evidence References
cytoplasm inferred from direct assay (Lin et al., 2008) cytoplasmic mRNA processing body inferred from direct assay (Zabolotskaya et al., 2008)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
5'-3' exoribonuclease activity inferred from sequence or structural similarity (Newbury, 1997) nucleic acid binding inferred from electronic annotation with InterPro:IPR004859 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
gastrulation non-traceable author statement (Morgan, 2002) RNA catabolic process non-traceable author statement (Morgan, 2002)
Cellular Component
CV term Evidence References
cytoplasm non-traceable author statement (Morgan, 2002)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions pcm allele Gene References
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
Orthologs
Genome-wide drosophilid orthologs	Dana\GF20490 Dere\GG18055 Dgri\GH17871 Dmoj\GI16439 Dper\GL14782 Dpse\GA17195 Dsec\GM22742 Dvir\GJ15840 Dwil\GK17975 Dyak\GE17387
Curated drosophilid orthologs	Dpse\GA17195
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • AAEL008814-PA Aedes aegypti (mosquito) AGAP004430-PA Anopheles gambiae (mosquito) XP_393481.2 Apis mellifera (honey bee) XP_001945621.1 Acyrthosiphon pisum (pea aphid) 34347 Batrachochytrium dendrobatidis (chytrid fungus) BGIBMGA000473-PA Bombyx mori (silk worm) ENSBTAP00000015318 Bos taurus (bovine) CN18416 Caenorhabditis brenneri (small nematode) CBP29401 Caenorhabditis briggsae (nematode) CE42924 Caenorhabditis elegans (worm) ENSCAFP00000011586 Canis familiaris (dog) JA15327 Caenorhabditis japonica (nematode) CMR447C Cyanidioschyzon merolae (red alga) cn05367 Cryptococcus neoformans (yeast-like fungus) cgd6_2080 Cryptosporidium parvum (protozoan parasite) CPIJ007753 Culex pipens (mosquito) RP29844 Caenorhabditis remanei (nematode) ENSCSAVP00000014690 Ciona savignyi (sedentary tunicate) DDB0237529 Dictyostelium discoideum (amoeba) ENSECAP00000006606 Equus caballus (horse) ENSGACP00000018914 Gymnopilus aculeatus (mushroom) ENSGALP00000004257 Gallus gallus (chicken) ENSP00000264951 Homo sapiens (human) ISCW019569-PA Ixodes scapularis (deer tick) 165314 Lottia gigantea (owl limpet) LmjF06.0260 Leishmania major (virus) ENSMODP00000026541 Monodelphis domestica (gray opossum) ENSMMUP00000018448 Macaca mulatta (rhesus monkey) ENSMUSP00000034981 Mus musculus (house mouse) 242212 Nematostella vectensis (starlet anemone) XP_001603129.1 Nasonia vitripennis (wasp) ENSOANP00000010746 Ornithorynchus anatinus (platypus) ENSORLP00000016296 Oryzias latipes (japanese killifish) PHUM005004-PA Pediculus humanus (human body louse) ENSPPYP00000015851 Pongo pygmaeus (orangutan) 78102 Phytophthora ramorum (sudden oak death pathogen) 130875 Phytophthora sojae (root rot pathogen) ENSPTRP00000026654 Pan troglodytes (chimpanzee) ENSRNOP00000014481 Rattus norvegicus (norway rat) YGL173C Saccharomyces cerevisiae (budding yeast) Smp_140420 Schistosoma mansoni (trematode parasite) SPAC17A5.14 Schizosaccharomyces pombe (fission yeast) XP_974750.2 Tribolium castaneum (red flour beetle) ENSTNIP00000004886 Tetraodon nigroviridis (green spotted pufferfish) ENSTRUP00000011685 Takifugu rubripes (pufferfish Takifugu) 91117.m00132 Trichomonas vaginalis (parasitic flagellated protozoan) YALI0C23144g Yarrowia lipolytica (nonconventional yeast) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • NV11538 NV10050 LH20026 ISCW019569 FBgn0234855 FBgn0219974 FBgn0203027 FBgn0177612 FBgn0077209 FBgn0152386 FBgn0139187 FBgn0125340 FBgn0110272 FBgn0097496 CPIJ007753 BGIBMGA000473 ACYPI004449 GB10706 AGAP004430 AAEL008814 PB23333 PHUM577340 GLEAN_13457
Stocks & Reagents
Stocks Listed in FlyBase ( 4 )
Bloomington	33263 w* P{EP}pcmG1726 34690 y1 sc* v1; P{TRiP.HMS01169}attP2
VDRC	v105739 P{KK108511}VIE-260B v21677 w1118; P{GD10926}v21677
Genomic Clones ( 2 )
	BACR10M08 BACR27L16 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 31 )
	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
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT01889 AT17440 AT19150 AT20701 AT23995 GH11392 GM02716 LD07262 LD24464 LD24588 LD29795 LD34993 LD42194 LD44093 LP20018
Other clones	44342 70204 75058 214319.52 214533.61 bs10f03 Dmel_neb_010182_0953_0738 Dmel_neb_014769_0698_3075 EK153603 EK159564 EK197318 EK204862 EP08531 LD26388 SD03153
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0020261 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 32935
Antibody Information
	polyclonal (Grima et al., 2008, Zabolotskaya et al., 2008)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity 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)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_078684 NM_001169325 RefSeq (Proteins) • NP_523408 NP_001162796 DDBJ / EMBL / GenBank • AA817398 AAF48958 AAK93099 ACZ95330 AI134050 AI945245 AJ242529 AW942649 AY051675 CAB43711 Entrez Gene - A searchable database of RefSeq genes. • 32935 UniProtKB/TrEMBL • E1JJR3 Q9VWI1 Q9XZU2
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Putative 5-3 exonuclease (IPR004859) 5'-3' exoribonuclease 1 (IPR016494)
Linkouts
	BioGRID - A database of protein and genetic interactions • 59237 DroID - A comprehensive database of gene and protein interactions. • FBgn0020261 DRSC - Results from 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 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0020261 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 32935 InParanoid A subset of ortholog calls from InParanoid. • AAEL008814-PA Aedes aegypti (mosquito) AGAP004430-PA Anopheles gambiae (mosquito) XP_393481.2 Apis mellifera (honey bee) XP_001945621.1 Acyrthosiphon pisum (pea aphid) 34347 Batrachochytrium dendrobatidis (chytrid fungus) BGIBMGA000473-PA Bombyx mori (silk worm) ENSBTAP00000015318 Bos taurus (bovine) CN18416 Caenorhabditis brenneri (small nematode) CBP29401 Caenorhabditis briggsae (nematode) CE42924 Caenorhabditis elegans (worm) ENSCAFP00000011586 Canis familiaris (dog) JA15327 Caenorhabditis japonica (nematode) CMR447C Cyanidioschyzon merolae (red alga) cn05367 Cryptococcus neoformans (yeast-like fungus) cgd6_2080 Cryptosporidium parvum (protozoan parasite) CPIJ007753 Culex pipens (mosquito) RP29844 Caenorhabditis remanei (nematode) ENSCSAVP00000014690 Ciona savignyi (sedentary tunicate) DDB0237529 Dictyostelium discoideum (amoeba) ENSECAP00000006606 Equus caballus (horse) ENSGACP00000018914 Gymnopilus aculeatus (mushroom) ENSGALP00000004257 Gallus gallus (chicken) ENSP00000264951 Homo sapiens (human) ISCW019569-PA Ixodes scapularis (deer tick) 165314 Lottia gigantea (owl limpet) LmjF06.0260 Leishmania major (virus) ENSMODP00000026541 Monodelphis domestica (gray opossum) ENSMMUP00000018448 Macaca mulatta (rhesus monkey) ENSMUSP00000034981 Mus musculus (house mouse) 242212 Nematostella vectensis (starlet anemone) XP_001603129.1 Nasonia vitripennis (wasp) ENSOANP00000010746 Ornithorynchus anatinus (platypus) ENSORLP00000016296 Oryzias latipes (japanese killifish) PHUM005004-PA Pediculus humanus (human body louse) ENSPPYP00000015851 Pongo pygmaeus (orangutan) 78102 Phytophthora ramorum (sudden oak death pathogen) 130875 Phytophthora sojae (root rot pathogen) ENSPTRP00000026654 Pan troglodytes (chimpanzee) ENSRNOP00000014481 Rattus norvegicus (norway rat) YGL173C Saccharomyces cerevisiae (budding yeast) Smp_140420 Schistosoma mansoni (trematode parasite) SPAC17A5.14 Schizosaccharomyces pombe (fission yeast) XP_974750.2 Tribolium castaneum (red flour beetle) ENSTNIP00000004886 Tetraodon nigroviridis (green spotted pufferfish) ENSTRUP00000011685 Takifugu rubripes (pufferfish Takifugu) 91117.m00132 Trichomonas vaginalis (parasitic flagellated protozoan) YALI0C23144g Yarrowia lipolytica (nonconventional yeast) InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 32935 modMine - Data generated by the modENCODE project. • FBgn0020261 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • NV11538 NV10050 LH20026 ISCW019569 FBgn0234855 FBgn0219974 FBgn0203027 FBgn0177612 FBgn0077209 FBgn0152386 FBgn0139187 FBgn0125340 FBgn0110272 FBgn0097496 CPIJ007753 BGIBMGA000473 ACYPI004449 GB10706 AGAP004430 AAEL008814 PB23333 PHUM577340 GLEAN_13457
Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym	CG3291 (Labourier et al., 2002, Hollien and Weissman, 2006, Keleman et al., 2009.8.5, Ni et al., 2010.12.1) pcm (Schneider et al., 2006, Lin et al., 2008, Lim et al., 2009, Grima et al., 2008, Zabolotskaya et al., 2008) Pcm (Kuan et al., 2009) XRN1 (Valencia-Sanchez and Maquat, 2004, Rehwinkel et al., 2005, Behm-Ansmant et al., 2007, Eulalio et al., 2007, Haas et al., 2010, Rehwinkel et al., 2005) Xrn1 (Bönisch et al., 2007) XRN1/pcm (Hollien and Weissman, 2006) Xrn1p (Valencia-Sanchez et al., 2006)
Name Synonym	Pacman (Morgan, 2002, Rehwinkel et al., 2005, Zaessinger et al., 2006, Barbee et al., 2006, Lin et al., 2008, Zabolotskaya et al., 2008) pacman (Newbury, 1999.5.25, Newbury and Till, 1997, Schneider et al., 2006, Lim et al., 2009, Grima et al., 2008, Lin et al., 2008)
Secondary FlyBase IDs
References ( 47 )
Generate a list of	All references relating to this gene ( 47 )
List References by type	Research paper  ( 17 ) Supplementary material  ( 5 ) Review  ( 3 ) Personal communication to FlyBase  ( 7 ) Abstract  ( 8 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 1 ) Curated genome annotation  ( 2 ) Computer file  ( 1 ) Automatic genome annotation  ( 1 )
Recent research papers ( 1 )
	Haas et al., 2010, J. Cell Biol. 189(2): 289--302 HPat provides a link between deadenylation and decapping in metazoa. [FBrf0210604] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...