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Gene Dmel\Pcf11

General Information
Symbol	Dmel\Pcf11	Species	D. melanogaster
Name	Pcf11	Annotation symbol	CG10228
Feature type	protein_coding_gene	FlyBase ID	FBgn0022063
Gene Model Status	Current	Stock availability	8 publicly available
Also Known As	l(2)k08015
Genomic Location
Chromosome (arm)	2R	Recombination map
Cytogenetic map	51C5-51C7	Sequence location	2R:10,748,661..10,758,575 [-]
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 Pcf11 is referred to in FlyBase by the symbol Dmel\Pcf11 (CG10228, FBgn0022063). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: RNA binding. There is experimental evidence that it is involved in the biological process: neurogenesis. 5 alleles are reported. The phenotypes of these alleles are annotated with: mesothoracic tergum; crystal cell. It has 4 annotated transcripts and 4 annotated polypeptides. Protein features are: Domain of unknown function DUF618; ENTH/VHS; RNA polymerase II, large subunit, CTD. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed at stages throughout embryogenesis, at stages throughout the pupal period, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult eye, larval/adult central nervous system, larval Malpighian tubules, larval/adult salivary gland, larval trachea, adult male accessory gland. Comments on Affy2 ProbeSet: ProbeSet 1638931_at completely aligns to an exonic region of only a subset of 2 of the 4 FlyBase-annotated transcript isoforms of Pcf11. Gene sequence location is 2R:10748661..10758575.
External Summaries
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	References Neumüller et al., 2011, Cell Stem Cell 8(5): 580--593
FB2012_01	Sequence features HFA05983 BKN45202 BKN20818
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 51C5-51C7   Limits computationally determined from genome sequence between P{lacW}Rpn6k00103 and P{PZ}chn02064
Experimentally Determined Cytological Location
Cytogenetic map Notes References 51D3-51D5   (determined by in situ hybridisation)   (Spradling et al., 1999) 51D3-51D5     (BDGP Project Members, 1994-1999)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Pcf11 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) Pcf11-RB FBtr0301513  NM_001169682   2646   573 Pcf11-RC FBtr0302109  NM_001169683   818   86 Pcf11-RD FBtr0302294  NM_137155   6320   1953 Pcf11-RE FBtr0302560  NM_001202002   5978   1839
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Pcf11-PB   FBpp0290728   63.3   573   10.70     NP_001163153   ACZ94425 Pcf11-PC   FBpp0291319   10.2   86   5.68     NP_001163154   ACZ94426 Pcf11-PD   FBpp0291500   212.8   1953   6.14     NP_610999   AAF58192 Pcf11-PE   FBpp0291716   200.9   1839   6.07     NP_001188931   ADV37177
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • RNA polymerase II, large subunit, CTD (IPR006569) ENTH/VHS (IPR008942) Domain of unknown function DUF618 (IPR006903)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA263680   AA540187   AA567123   AA567896   AA698671   AA817665   AA942456   AA950180   AA978927   AE013599 AAF58192   AE013599 ACZ94425   AE013599 ACZ94426   AE013599 ADV37177   AI455434   AI455910   AI456805   AQ025854   AX094022   AY075387   AY231688   BG638769   BI356805   BI637966   BI640721   BP552362   BP552363   BP560122   BT001647 AAN71402   BT064645   BT088974   BT099611   CK605000   CO188515   CO188730   CO190024   CO265445   CO265637   CO267802   CO268449   CO270645   CO272495   CO272733   CO283101   CO287679   CO293696   CO294095   CO301148   CO308272   CO319251   CO321059   CO325812   CO331221   CO333822   CO342228   CO343232   EC066902   EC068346   EC071850   EC084074   EC086749   EC197142   EC197330   EC199646   EC200238   EC204287   EC204387   EC206718   EC206763   EC210614   EC218906   EC221698   EC238187   EC241316   EC244682   EC255554   EC256151   EL869910   EW712640   FE426491   FE426575   FE862718   FE862988   FE863177   FE863208   FE863273
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q8IGR2 A1Z9W4 E1JH68 C0P8M6
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
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
mass spectroscopy Stage Tissue/Position (including subcellular localization) Reference day 5 of adulthood & male -- day 7 of adulthood & male   spermatozoon   (Wasbrough et al., 2010)
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 FBgn0022063    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0022063 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 moderately high expression to a trough of moderate expression. Peak expression observed at stages throughout embryogenesis, at stages throughout the pupal period, in adult female 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 FBgn0022063 expression level Developmental Stage   Expression Level embryo 00-02hr    1951 embryo 02-04hr    2711 embryo 04-06hr    2261 embryo 06-08hr    2805 embryo 08-10hr    2414 embryo 10-12hr    2162 embryo 12-14hr    1861 embryo 14-16hr    1894 embryo 16-18hr    1866 embryo 18-20hr    1677 embryo 20-22hr    2020 embryo 22-24hr    1720 larva L1    956 larva L2    745 larva L3 12hr old    684 larva L3 puffstage 1-2    800 larva L3 puffstage 3-6    1220 larva L3 puffstage 7-9    1394 white prepupae new    1614 white prepupae 12hr    1566 white prepupae 24hr    1903 pupae 2d postWPP    1584 pupae 3d postWPP    1024 pupae 4d postWPP    1140 adult male 01day    1025 adult male 05day    1226 adult male 30day    1275 adult female 01day    1178 adult female 05day    1464 adult female 30day    1481 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (1951) embryo 02-04hr  (2711) embryo 04-06hr  (2261) embryo 06-08hr  (2805) embryo 08-10hr  (2414) embryo 10-12hr  (2162) embryo 12-14hr  (1861) embryo 14-16hr  (1894) embryo 16-18hr  (1866) embryo 18-20hr  (1677) embryo 20-22hr  (2020) embryo 22-24hr  (1720) larva L1  (956) larva L2  (745) larva L3 12hr old  (684) larva L3 puffstage 1-2  (800) larva L3 puffstage 3-6  (1220) larva L3 puffstage 7-9  (1394) white prepupae new  (1614) white prepupae 12hr  (1566) white prepupae 24hr  (1903) pupae 2d postWPP  (1584) pupae 3d postWPP  (1024) pupae 4d postWPP  (1140) adult male 01day  (1025) adult male 05day  (1226) adult male 30day  (1275) adult female 01day  (1178) adult female 05day  (1464) adult female 30day  (1481) Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (1951) embryo 02-04hr  (2711) embryo 04-06hr  (2261) embryo 06-08hr  (2805) embryo 08-10hr  (2414) embryo 10-12hr  (2162) embryo 12-14hr  (1861) embryo 14-16hr  (1894) embryo 16-18hr  (1866) embryo 18-20hr  (1677) embryo 20-22hr  (2020) embryo 22-24hr  (1720) larva L1    956 larva L2    745 larva L3 12hr old    684 larva L3 puffstage 1-2    800 larva L3 puffstage 3-6    1220 larva L3 puffstage 7-9    1394 white prepupae new  (1614) white prepupae 12hr  (1566) white prepupae 24hr  (1903) pupae 2d postWPP  (1584) pupae 3d postWPP    1024 pupae 4d postWPP    1140 adult male 01day    1025 adult male 05day    1226 adult male 30day    1275 adult female 01day    1178 adult female 05day  1464 adult female 30day  1481 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    1951 embryo 02-04hr    2711 embryo 04-06hr    2261 embryo 06-08hr    2805 embryo 08-10hr    2414 embryo 10-12hr    2162 embryo 12-14hr    1861 embryo 14-16hr    1894 embryo 16-18hr    1866 embryo 18-20hr    1677 embryo 20-22hr    2020 embryo 22-24hr    1720 larva L1    956 larva L2    745 larva L3 12hr old    684 larva L3 puffstage 1-2    800 larva L3 puffstage 3-6    1220 larva L3 puffstage 7-9    1394 white prepupae new    1614 white prepupae 12hr    1566 white prepupae 24hr    1903 pupae 2d postWPP    1584 pupae 3d postWPP    1024 pupae 4d postWPP    1140 adult male 01day    1025 adult male 05day    1226 adult male 30day    1275 adult female 01day    1178 adult female 05day    1464 adult female 30day    1481 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    1951 embryo 02-04hr    2711 embryo 04-06hr    2261 embryo 06-08hr    2805 embryo 08-10hr    2414 embryo 10-12hr    2162 embryo 12-14hr    1861 embryo 14-16hr    1894 embryo 16-18hr    1866 embryo 18-20hr    1677 embryo 20-22hr    2020 embryo 22-24hr    1720 larva L1    956 larva L2    745 larva L3 12hr old    684 larva L3 puffstage 1-2    800 larva L3 puffstage 3-6    1220 larva L3 puffstage 7-9    1394 white prepupae new    1614 white prepupae 12hr    1566 white prepupae 24hr    1903 pupae 2d postWPP    1584 pupae 3d postWPP    1024 pupae 4d postWPP    1140 adult male 01day    1025 adult male 05day    1226 adult male 30day    1275 adult female 01day    1178 adult female 05day    1464 adult female 30day    1481 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0022063 expression level Developmental Stage   Expression Level embryo 00-02hr    1951 embryo 02-04hr    2711 embryo 04-06hr    2261 embryo 06-08hr    2805 embryo 08-10hr    2414 embryo 10-12hr    2162 embryo 12-14hr    1861 embryo 14-16hr    1894 embryo 16-18hr    1866 embryo 18-20hr    1677 embryo 20-22hr    2020 embryo 22-24hr    1720 larva L1    956 larva L2    745 larva L3 12hr old    684 larva L3 puffstage 1-2    800 larva L3 puffstage 3-6    1220 larva L3 puffstage 7-9    1394 white prepupae new    1614 white prepupae 12hr    1566 white prepupae 24hr    1903 pupae 2d postWPP    1584 pupae 3d postWPP    1024 pupae 4d postWPP    1140 adult male 01day    1025 adult male 05day    1226 adult male 30day    1275 adult female 01day    1178 adult female 05day    1464 adult female 30day    1481 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  (1951) embryo 02-04hr  (2711) embryo 04-06hr  (2261) embryo 06-08hr  (2805) embryo 08-10hr  (2414) embryo 10-12hr  (2162) embryo 12-14hr  (1861) embryo 14-16hr  (1894) embryo 16-18hr  (1866) embryo 18-20hr  (1677) embryo 20-22hr  (2020) embryo 22-24hr  (1720) larva L1  (956) larva L2  (745) larva L3 12hr old  (684) larva L3 puffstage 1-2  (800) larva L3 puffstage 3-6  (1220) larva L3 puffstage 7-9  (1394) white prepupae new  (1614) white prepupae 12hr  (1566) white prepupae 24hr  (1903) pupae 2d postWPP  (1584) pupae 3d postWPP  (1024) pupae 4d postWPP  (1140) adult male 01day  (1025) adult male 05day  (1226) adult male 30day  (1275) adult female 01day  (1178) adult female 05day  (1464) adult female 30day  (1481) Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  1951 embryo 02-04hr  (2711) embryo 04-06hr  2261 embryo 06-08hr  (2805) embryo 08-10hr  2414 embryo 10-12hr  2162 embryo 12-14hr  1861 embryo 14-16hr  1894 embryo 16-18hr  1866 embryo 18-20hr  1677 embryo 20-22hr  2020 embryo 22-24hr  1720 larva L1    956 larva L2    745 larva L3 12hr old    684 larva L3 puffstage 1-2    800 larva L3 puffstage 3-6    1220 larva L3 puffstage 7-9    1394 white prepupae new  1614 white prepupae 12hr  1566 white prepupae 24hr  1903 pupae 2d postWPP  1584 pupae 3d postWPP    1024 pupae 4d postWPP    1140 adult male 01day    1025 adult male 05day    1226 adult male 30day    1275 adult female 01day    1178 adult female 05day  1464 adult female 30day  1481 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    1951 embryo 02-04hr    2711 embryo 04-06hr    2261 embryo 06-08hr    2805 embryo 08-10hr    2414 embryo 10-12hr    2162 embryo 12-14hr    1861 embryo 14-16hr    1894 embryo 16-18hr    1866 embryo 18-20hr    1677 embryo 20-22hr    2020 embryo 22-24hr    1720 larva L1    956 larva L2    745 larva L3 12hr old    684 larva L3 puffstage 1-2    800 larva L3 puffstage 3-6    1220 larva L3 puffstage 7-9    1394 white prepupae new    1614 white prepupae 12hr    1566 white prepupae 24hr    1903 pupae 2d postWPP    1584 pupae 3d postWPP    1024 pupae 4d postWPP    1140 adult male 01day    1025 adult male 05day    1226 adult male 30day    1275 adult female 01day    1178 adult female 05day    1464 adult female 30day    1481 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    1951 embryo 02-04hr    2711 embryo 04-06hr    2261 embryo 06-08hr    2805 embryo 08-10hr    2414 embryo 10-12hr    2162 embryo 12-14hr    1861 embryo 14-16hr    1894 embryo 16-18hr    1866 embryo 18-20hr    1677 embryo 20-22hr    2020 embryo 22-24hr    1720 larva L1    956 larva L2    745 larva L3 12hr old    684 larva L3 puffstage 1-2    800 larva L3 puffstage 3-6    1220 larva L3 puffstage 7-9    1394 white prepupae new    1614 white prepupae 12hr    1566 white prepupae 24hr    1903 pupae 2d postWPP    1584 pupae 3d postWPP    1024 pupae 4d postWPP    1140 adult male 01day    1025 adult male 05day    1226 adult male 30day    1275 adult female 01day    1178 adult female 05day    1464 adult female 30day    1481 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 FBgn0022063    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0022063 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: adult eye, larval/adult central nervous system, larval Malpighian tubules, larval/adult salivary gland, larval trachea, adult male accessory gland. [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 FBgn0022063 expression level Tissue   Expression Level Larval Central Nervous System    113.525 Larval Midgut    80.6 Larval Hindgut    75.2 Larval Malpighian Tubules    104.1 Larval Fat Body    89.6 Larval Salivary Gland    213.5 Larval Trachea    128.225 Larval Carcass    77.925 Adult Head    61.7 Adult Eye    107.8 Adult Brain    159.9 Adult Thoracic-Abdominal Ganglion    108.5 Adult Crop    89.8 Adult Midgut    73.4 Adult Hindgut    91 Adult Malpighian Tubules    90.9 Adult Fat Body    73.3 Adult Salivary Gland    152.6 Adult Heart    77.05 Adult VirginFemale Spermatheca    71.8 Adult InseminatedFemale Spermatheca    70.3 Adult Ovary    76.2 Adult Testis no informative data Adult Male Accessory Gland    117.5 Adult Carcass    96.2 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    113.525 Larval Midgut    80.6 Larval Hindgut    75.2 Larval Malpighian Tubules    104.1 Larval Fat Body    89.6 Larval Salivary Gland    213.5 Larval Trachea    128.225 Larval Carcass    77.925 Adult Head    61.7 Adult Eye    107.8 Adult Brain    159.9 Adult Thoracic-Abdominal Ganglion    108.5 Adult Crop    89.8 Adult Midgut    73.4 Adult Hindgut    91 Adult Malpighian Tubules    90.9 Adult Fat Body    73.3 Adult Salivary Gland    152.6 Adult Heart    77.05 Adult VirginFemale Spermatheca    71.8 Adult InseminatedFemale Spermatheca    70.3 Adult Ovary    76.2 Adult Testis no informative data Adult Male Accessory Gland    117.5 Adult Carcass    96.2 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    113.525 Larval Midgut    80.6 Larval Hindgut    75.2 Larval Malpighian Tubules    104.1 Larval Fat Body    89.6 Larval Salivary Gland    213.5 Larval Trachea    128.225 Larval Carcass    77.925 Adult Head    61.7 Adult Eye    107.8 Adult Brain    159.9 Adult Thoracic-Abdominal Ganglion    108.5 Adult Crop    89.8 Adult Midgut    73.4 Adult Hindgut    91 Adult Malpighian Tubules    90.9 Adult Fat Body    73.3 Adult Salivary Gland    152.6 Adult Heart    77.05 Adult VirginFemale Spermatheca    71.8 Adult InseminatedFemale Spermatheca    70.3 Adult Ovary    76.2 Adult Testis no informative data Adult Male Accessory Gland    117.5 Adult Carcass    96.2 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    113.525 Larval Midgut    80.6 Larval Hindgut    75.2 Larval Malpighian Tubules    104.1 Larval Fat Body    89.6 Larval Salivary Gland    213.5 Larval Trachea    128.225 Larval Carcass    77.925 Adult Head    61.7 Adult Eye    107.8 Adult Brain    159.9 Adult Thoracic-Abdominal Ganglion    108.5 Adult Crop    89.8 Adult Midgut    73.4 Adult Hindgut    91 Adult Malpighian Tubules    90.9 Adult Fat Body    73.3 Adult Salivary Gland    152.6 Adult Heart    77.05 Adult VirginFemale Spermatheca    71.8 Adult InseminatedFemale Spermatheca    70.3 Adult Ovary    76.2 Adult Testis no informative data Adult Male Accessory Gland    117.5 Adult Carcass    96.2 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0022063 expression level Tissue   Expression Level Larval Central Nervous System    113.525 Larval Midgut    80.6 Larval Hindgut    75.2 Larval Malpighian Tubules    104.1 Larval Fat Body    89.6 Larval Salivary Gland    213.5 Larval Trachea    128.225 Larval Carcass    77.925 Adult Head    61.7 Adult Eye    107.8 Adult Brain    159.9 Adult Thoracic-Abdominal Ganglion    108.5 Adult Crop    89.8 Adult Midgut    73.4 Adult Hindgut    91 Adult Malpighian Tubules    90.9 Adult Fat Body    73.3 Adult Salivary Gland    152.6 Adult Heart    77.05 Adult VirginFemale Spermatheca    71.8 Adult InseminatedFemale Spermatheca    70.3 Adult Ovary    76.2 Adult Testis no informative data Adult Male Accessory Gland    117.5 Adult Carcass    96.2 Expression Level Scale  None   Low   Moderate  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    113.525 Larval Midgut    80.6 Larval Hindgut    75.2 Larval Malpighian Tubules    104.1 Larval Fat Body    89.6 Larval Salivary Gland    213.5 Larval Trachea    128.225 Larval Carcass    77.925 Adult Head    61.7 Adult Eye    107.8 Adult Brain    159.9 Adult Thoracic-Abdominal Ganglion    108.5 Adult Crop    89.8 Adult Midgut    73.4 Adult Hindgut    91 Adult Malpighian Tubules    90.9 Adult Fat Body    73.3 Adult Salivary Gland    152.6 Adult Heart    77.05 Adult VirginFemale Spermatheca    71.8 Adult InseminatedFemale Spermatheca    70.3 Adult Ovary    76.2 Adult Testis no informative data Adult Male Accessory Gland    117.5 Adult Carcass    96.2 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    113.525 Larval Midgut    80.6 Larval Hindgut    75.2 Larval Malpighian Tubules    104.1 Larval Fat Body    89.6 Larval Salivary Gland    213.5 Larval Trachea    128.225 Larval Carcass    77.925 Adult Head    61.7 Adult Eye    107.8 Adult Brain    159.9 Adult Thoracic-Abdominal Ganglion    108.5 Adult Crop    89.8 Adult Midgut    73.4 Adult Hindgut    91 Adult Malpighian Tubules    90.9 Adult Fat Body    73.3 Adult Salivary Gland    152.6 Adult Heart    77.05 Adult VirginFemale Spermatheca    71.8 Adult InseminatedFemale Spermatheca    70.3 Adult Ovary    76.2 Adult Testis no informative data Adult Male Accessory Gland    117.5 Adult Carcass    96.2 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    113.525 Larval Midgut    80.6 Larval Hindgut    75.2 Larval Malpighian Tubules    104.1 Larval Fat Body    89.6 Larval Salivary Gland    213.5 Larval Trachea    128.225 Larval Carcass    77.925 Adult Head    61.7 Adult Eye    107.8 Adult Brain    159.9 Adult Thoracic-Abdominal Ganglion    108.5 Adult Crop    89.8 Adult Midgut    73.4 Adult Hindgut    91 Adult Malpighian Tubules    90.9 Adult Fat Body    73.3 Adult Salivary Gland    152.6 Adult Heart    77.05 Adult VirginFemale Spermatheca    71.8 Adult InseminatedFemale Spermatheca    70.3 Adult Ovary    76.2 Adult Testis no informative data Adult Male Accessory Gland    117.5 Adult Carcass    96.2 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 no informative data Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    61.7   NA  Eye    107.8   NA  Brain    159.9   113.525  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    108.5   NA  Crop    89.8   80.6  Midgut    73.4   75.2  Hindgut    91   104.1  Malpighian Tubules    90.9   89.6  Fat Body    73.3   213.5  Salivary Gland    152.6   NA  Heart    77.05   128.225  Trachea    NA   NA  VirginFemale Spermatheca    71.8   NA  InseminatedFemale Spermatheca    70.3   NA  Ovary    76.2   NA  Testis    no informative data   NA  Male Accessory Gland    117.5   77.925  Carcass    96.2 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_27
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0022063 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG10228-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal, with Scer\GAL41407 Pcf11GD6907 lethal | recessive Pcf11k08015 Pcf11k08023 semi-lethal | pupal stage, with Scer\GAL4pnr-MD237 Pcf11GD6907 Other Phenotypes Allele body color defective, with Scer\GAL4pnr-MD237 Pcf11GD6907 neuroanatomy defective | larval stage, with Scer\GAL41407 Pcf11GD6907 visible, with Scer\GAL4pnr-MD237 Pcf11GD6907 Phenotype manifest in Allele crystal cell Pcf11k08015 embryonic/larval neuroblast | larval stage, with Scer\GAL41407 Pcf11GD6907 ganglion mother cell | larval stage, with Scer\GAL41407 Pcf11GD6907 mesothoracic tergum, with Scer\GAL4pnr-MD237 Pcf11GD6907
Classical Alleles ( 2 )
For All Classical Alleles Show
Allele of Pcf11 Class Mutagen Stocks Known lesion Pcf11k08015 P-element activity 2 -- Pcf11k08023 P-element activity 1 --
Alleles Carried on Transgenic Constructs ( 3 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Pcf11 Class Mutagen Stocks Known lesion Pcf11GD6907 in vitro construct - RNAi in vitro construct - regulatory fusion 3 Yes Pcf11HMS00406 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Pcf11KK100722 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes
Aneuploid Aberrations
Not disrupted in	Df(2R)Jp1 (Spradling et al., 1999, Sekelsky, 1999.9.21, Sekelsky et al., 2000, BDGP Project Members, 1994-1999) Df(2R)Jp4 (Sekelsky et al., 2000) Df(2R)XTE-18 (Sekelsky et al., 2000)
Disrupted in	Df(2R)EP2590-Δ1 (Dworak et al., 2001) Df(2R)EP2590-Δ11 (Dworak et al., 2001) Df(2R)EP2590-Δ14 (Dworak et al., 2001) Df(2R)knSA3 (Sekelsky, 1999.9.21, Sekelsky et al., 2000)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD6907} NA P{KK100722} NA P{TRiP.HMS00406} NA
Insertions
	Type of insertions Name Expression data insertion of enhancer trap P{lacW}l(2)SH1522SH1522 No P{lacW}Pcf11k08015 No P{lacW}Pcf11k08023 No
Gene Ontology: Function, Process & Cellular Component ( 4 unique terms )
Terms Based on Experimental Evidence ( 2 terms )
Molecular Function
CV term Evidence References
RNA binding inferred from direct assay (Zhang and Gilmour, 2006)
Biological Process
CV term Evidence References
neurogenesis inferred from mutant phenotype (Neumüller et al., 2011)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 2 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
mRNA cleavage inferred from sequence or structural similarity with NCBI:NP_010514 (Mount and Salz, 2000)
Cellular Component
CV term Evidence References
mRNA cleavage factor complex inferred from sequence or structural similarity with NCBI:NP_010514 (Mount and Salz, 2000)
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 Pcf11 allele Gene References
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 62402 DroID - A comprehensive database of gene and protein interactions. • FBgn0022063 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 36658
Orthologs
Genome-wide drosophilid orthologs	Dana\GF12082 Dere\GG22388 Dgri\GH22985 Dmoj\GI18953 Dper\GL17525 Dpse\GA24192 Dsec\GM20171 Dsim\GD25648 Dvir\GJ21559 Dwil\GK22121 Dyak\GE12277
Curated drosophilid orthologs	Dpse\GA10172   Dyak\GE12277
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • AAEL011663-PA Aedes aegypti (mosquito) AGAP001271-PA Anopheles gambiae (mosquito) XP_392839.3 Apis mellifera (honey bee) XP_001945368.1 Acyrthosiphon pisum (pea aphid) At4g04885.1 Arabidopsis thaliana (wall cress) ENSBTAP00000020320 Bos taurus (bovine) CN02507 Caenorhabditis brenneri (small nematode) CE02032 Caenorhabditis elegans (worm) ENSCAFP00000006880 Canis familiaris (dog) CMG045C Cyanidioschyzon merolae (red alga) CPIJ001187 Culex pipens (mosquito) ENSCPOP00000003702 Cavia porcellus (guinea pig) 222735 Capitella spl (polychaete worm) 254414 Daphnia pulex (daphnia) ENSDARP00000065561 Danio rerio (zebra fish) ENSECAP00000016536 Equus caballus (horse) ENSGACP00000027636 Gymnopilus aculeatus (mushroom) ENSGALP00000027831 Gallus gallus (chicken) ENSP00000298281 Homo sapiens (human) ISCW009703-PA Ixodes scapularis (deer tick) ENSMODP00000005550 Monodelphis domestica (gray opossum) ENSMMUP00000006658 Macaca mulatta (rhesus monkey) ENSMUSP00000044036 Mus musculus (house mouse) XP_001605349.1 Nasonia vitripennis (wasp) ENSOANP00000010456 Ornithorynchus anatinus (platypus) ENSORLP00000017214 Oryzias latipes (japanese killifish) LOC_Os09g39270.1 Oryza sativa (asian rice) PHUM006054-PA Pediculus humanus (human body louse) PP07239 Pristionchus pacificus (nematode) 98034 Physcomitrella patens (moss) ENSPPYP00000004264 Pongo pygmaeus (orangutan) 143093 Phytophthora sojae (root rot pathogen) 196707 Populus trichocarpa (black cottonwood) ENSPTRP00000007096 Pan troglodytes (chimpanzee) ENSRNOP00000013552 Rattus norvegicus (norway rat) XP_787458.2 Strongylocentrotus purpuratus (purple sea urchin) XP_970852.2 Tribolium castaneum (red flour beetle) ENSTNIP00000007432 Tetraodon nigroviridis (green spotted pufferfish) ENSTRUP00000010505 Takifugu rubripes (pufferfish Takifugu) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • PB14005 PB11524 NV16871 NV16869 NV16870 LH15740 ISCW009702 ISCW009703 ISCW009701 FBgn0068516 FBgn0224106 FBgn0208679 FBgn0196933 FBgn0186900 FBgn0175054 JGI_V11_216053 JGI_V11_254414 FBgn0245591 FBgn0163831 FBgn0161667 FBgn0160936 FBgn0155128 FBgn0141692 FBgn0130442 FBgn0114560 FBgn0089121 CPIJ001185 CPIJ001186 CPIJ001187 BGIBMGA009372 ACYPI004003 GB12825 AGAP001271 AAEL011663 PHUM005980 GLEAN_08263
Stocks & Reagents
Stocks Listed in FlyBase ( 8 )
Bloomington	32411 y1 sc* v1; P{TRiP.HMS00406}attP2 10756 y1 w67c23; P{lacW}Pcf11k08015/CyO
Kyoto	102613 y1 w67c23 ; P{lacW}Pcf11k08023 / CyO 111233 yd2 w1118 P{ey-FLP.N}2 P{GMR-lacZ.C(38.1)}TPN1; P{neoFRT}42D P{lacW}Pcf11k08015 /CyO y+
VDRC	v103710 P{KK100722}VIE-260B v38365 w1118; P{GD6907}v38365 v38366 w1118; P{GD6907}v38366 v44115 w1118; P{GD6907}v44115
Genomic Clones ( 1 )
	BACR03K23 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 72 )
	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	LD11480 LD24195 LD33071 RE43027
Other clones	MIP05908
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GM01150 HL01960 HL05452 LD06854 LD19585 LD26686 LD30123 LD33132 LD36938 SD20178 SD23706 UT01606
Other clones	8810 17514 31991 32689 38820 45868 57980 74413 153785 166111 172937 173622 214311.69 214569.60 CK01.50D.F1 CK01.51A.E8 CK01.57D.D5 CK01.83B.H6 CK01.117C.D8 CK01.119D.F4 CK01.128C.G1 EK040652 EK041721 EK046015 EK066463 EK091354 EK099625 EK107401 EK108157 EK142663 EK143250 EK151858 EK162244 EK180239 EK204143 EK206005 EK257260 EK277443 EK290231 EK298840 EK308107 EP02555 EP14209 EP16346 FGM218C12 FGM324G08 IP02052 LD35642 RM05183 RM05683 RM05983 RM06283 RM06383 RM06483 RM06583
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0022063 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 36658
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: Pcf11 l(2)k08015 (Zhang and Gilmour, 2006)
Source for database merge of	Source for merge of: l(2)k08015 anon-WO0118547.146 (FlyBase, 1996-) Source for merge of: l(2)k08015 CG10228 (Mutsuddi et al., 2004)
Additional comments	Source for merge of l(2)k08015 anon-WO0118547.146 was sequence comparison (date:051113). (FlyBase, 1996-)
Other Comments
	dsRNA made from templates generated with primers directed against this gene. (Zhang and Gilmour, 2006) Pcf11 inhibits transcription elongation by PolIIA under conditions that promote pausing. (Zhang and Gilmour, 2006) 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) Area matching Drosophila EST AA978927. This EST has sequence similarity to human PCF11p homolgue. (Davies, 2001.3.15)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_137155 NM_001169682 NM_001169683 NM_001202002 RefSeq (Proteins) • NP_610999 NP_001163153 NP_001163154 NP_001188931 DDBJ / EMBL / GenBank • AA817665 AA978927 AAF58192 AAN71402 ACZ94425 ACZ94426 ADV37177 AI455434 AQ025854 AX094022 AY075387 BI356805 BT001647 Entrez Gene - A searchable database of RefSeq genes. • 36658 UniProtKB/TrEMBL • A1Z9W4 C0P8M6 E1JH68 Q8IGR2
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • RNA polymerase II, large subunit, CTD (IPR006569) ENTH/VHS (IPR008942) Domain of unknown function DUF618 (IPR006903)
Linkouts
	BioGRID - A database of protein and genetic interactions • 62402 DroID - A comprehensive database of gene and protein interactions. • FBgn0022063 DRSC - Results from RNAi screens. • FBgn0022063 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0022063 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG10228-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0022063 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 36658 InParanoid A subset of ortholog calls from InParanoid. • AAEL011663-PA Aedes aegypti (mosquito) AGAP001271-PA Anopheles gambiae (mosquito) XP_392839.3 Apis mellifera (honey bee) XP_001945368.1 Acyrthosiphon pisum (pea aphid) At4g04885.1 Arabidopsis thaliana (wall cress) ENSBTAP00000020320 Bos taurus (bovine) CN02507 Caenorhabditis brenneri (small nematode) CE02032 Caenorhabditis elegans (worm) ENSCAFP00000006880 Canis familiaris (dog) CMG045C Cyanidioschyzon merolae (red alga) CPIJ001187 Culex pipens (mosquito) ENSCPOP00000003702 Cavia porcellus (guinea pig) 222735 Capitella spl (polychaete worm) 254414 Daphnia pulex (daphnia) ENSDARP00000065561 Danio rerio (zebra fish) ENSECAP00000016536 Equus caballus (horse) ENSGACP00000027636 Gymnopilus aculeatus (mushroom) ENSGALP00000027831 Gallus gallus (chicken) ENSP00000298281 Homo sapiens (human) ISCW009703-PA Ixodes scapularis (deer tick) ENSMODP00000005550 Monodelphis domestica (gray opossum) ENSMMUP00000006658 Macaca mulatta (rhesus monkey) ENSMUSP00000044036 Mus musculus (house mouse) XP_001605349.1 Nasonia vitripennis (wasp) ENSOANP00000010456 Ornithorynchus anatinus (platypus) ENSORLP00000017214 Oryzias latipes (japanese killifish) LOC_Os09g39270.1 Oryza sativa (asian rice) PHUM006054-PA Pediculus humanus (human body louse) PP07239 Pristionchus pacificus (nematode) 98034 Physcomitrella patens (moss) ENSPPYP00000004264 Pongo pygmaeus (orangutan) 143093 Phytophthora sojae (root rot pathogen) 196707 Populus trichocarpa (black cottonwood) ENSPTRP00000007096 Pan troglodytes (chimpanzee) ENSRNOP00000013552 Rattus norvegicus (norway rat) XP_787458.2 Strongylocentrotus purpuratus (purple sea urchin) XP_970852.2 Tribolium castaneum (red flour beetle) ENSTNIP00000007432 Tetraodon nigroviridis (green spotted pufferfish) ENSTRUP00000010505 Takifugu rubripes (pufferfish Takifugu) Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /genebrief/pcf11.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 36658 modMine - Data generated by the modENCODE project. • FBgn0022063 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • PB14005 PB11524 NV16871 NV16869 NV16870 LH15740 ISCW009702 ISCW009703 ISCW009701 FBgn0068516 FBgn0224106 FBgn0208679 FBgn0196933 FBgn0186900 FBgn0175054 JGI_V11_216053 JGI_V11_254414 FBgn0245591 FBgn0163831 FBgn0161667 FBgn0160936 FBgn0155128 FBgn0141692 FBgn0130442 FBgn0114560 FBgn0089121 CPIJ001185 CPIJ001186 CPIJ001187 BGIBMGA009372 ACYPI004003 GB12825 AGAP001271 AAEL011663 PHUM005980 GLEAN_08263
Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym	anon-WO0118547.146   CG10228 (Milchanowski et al., 2004, Mount and Salz, 2000, Keleman et al., 2009.8.5, Ni et al., 2010.12.1) dPcf11 (Zhang and Gilmour, 2006) l(2)k08015 (Sekelsky et al., 2000, Dworak et al., 2001, FlyBase, 1996-, Mutsuddi et al., 2004, Spradling et al., 1999, Davies et al., 2001) Pcf11 (Yao et al., 2007, Wasbrough et al., 2010, Neumüller et al., 2011) pcf11 (Zhou et al., 2008)
Name Synonym	lethal (2) k08015   Pcf11
Secondary FlyBase IDs
	FBgn0033975 FBgn0062215
References ( 25 )
Generate a list of	All references relating to this gene ( 25 )
List References by type	Research paper  ( 10 ) Supplementary material  ( 6 ) Personal communication to FlyBase  ( 4 ) FlyBase analysis  ( 1 ) Patent  ( 1 ) DNA/RNA sequence record  ( 1 ) Computer file  ( 2 )
Recent research papers ( 1 )
	Neumüller et al., 2011, Cell Stem Cell 8(5): 580--593 Genome-Wide Analysis of Self-Renewal in Drosophila Neural Stem Cells by Transgenic RNAi. [FBrf0213621] Show all research papers ...