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Gene Dmel\prd

General Information
Symbol	Dmel\prd	Species	D. melanogaster
Name	paired	Annotation symbol	CG6716
Feature type	protein_coding_gene	FlyBase ID	FBgn0003145
Gene Model Status	Current	Stock availability	21 publicly available
Genomic Location
Chromosome (arm)	2L	Recombination map	2-45
Cytogenetic map	33C3-33C3	Sequence location	2L:12,082,997..12,085,792 [-]
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 paired is referred to in FlyBase by the symbol Dmel\prd (CG6716, FBgn0003145). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: RNA polymerase II regulatory region sequence-specific DNA binding; sequence-specific distal enhancer binding RNA polymerase II transcription factor activity. There is experimental evidence that it is involved in the biological process: positive regulation of transcription from RNA polymerase II promoter. 73 alleles are reported. The phenotypes of these alleles are annotated with: organ system; organ system subdivision; cuticle; abdominal ventral denticle belt; embryonic/larval neuron; larval abdominal segment; thoracic segment; peripheral nervous system; metathoracic ventral denticle belt; gland; nervous system; adult; heart primordium; embryonic segment; epithelial furrow; external compound sense organ; syncytial blastoderm embryo; antennal segment. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: Homeobox; Homeobox, conserved site; Homeodomain-like; Homeodomain-related; Paired box protein, N-terminal; Winged helix-turn-helix transcription repressor DNA-binding. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of no expression detected. Peak expression observed within 00-06 hour embryonic stages, in adult male stages. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult male accessory gland. Comments on Affy2 ProbeSet: ProbeSet 1633879_a_at completely aligns to an exonic region common to each of the 2 FlyBase-annotated transcript isoforms of prd. Gene sequence location is 2L:12082997..12085792.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	prd: paired The wild-type allele of prd is required for normal segmentation in embryos and larvae. Mutant alleles and deficiencies show no maternal effects and are embryonic lethals with half the normal number of segmental units. In strong mutants, the anterior part of segments T1, T3, A2, A4, A6, and A8 and the posterior part of T2, A1, A3, A5, and A7 (i.e., odd-numbered parasegments) are deleted (Nusslein-Volhard et al., 1985). Weak mutants such as prd2 show small and less regular segmental deletions. Structures missing in prd mutants include: derivatives of the mandibular segments, labial sense organs, anterior prothorax, posterior mesothorax, anterior metathorax, and alternating posterior and anterior abdominal segments, including the telson and the posterior lateral sense organs (Nusslein-Volhard et al., 1985). No head fold visible at gastrulation. Experiments with a temperature-sensitive mutant indicate that the TSP occurs during the cellular blastoderm stage (Nusslein-Volhard et al., 1985; Kilchherr et al., 1986).
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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FB2012_01	References Kazemian et al., 2010, PLoS Biol. 8(8): Tchuraev and Galimzyanov, 2009, J. Theor. Biol. 259(4): 659--669 Fowlkes et al., 2011, PLoS Genet. 7(10): e1002346 Cunha et al., 2010, PLoS Genet. 6: e1001014 Sequence features BKN29894 HFA03597 Controlled Vocabulary Terms positive regulation of transcription from RNA polymerase II promoter RNA polymerase II regulatory region sequence-specific DNA binding sequence-specific distal enhancer binding RNA polymerase II transcription factor activity
FB2011_10	References Grad et al., 2004, Bioinformatics 20(16): 2738--2750 Zamparo and Perkins, 2009, Bioinformatics 25(20): 2670--2676
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 33C3-33C3   Limits computationally determined from genome sequence between P{EP}JhI-21EP1187 and P{lacW}Aats-thrk04203
Experimentally Determined Cytological Location
Cytogenetic map Notes References 33B1-33C1   (determined by in situ hybridisation)   (Kilchherr et al., 1986) 33C1-33C1   (determined by in situ hybridisation)   (Frigerio et al., 1986)
Experimentally Determined Recombination Data
Location	2-45 (Tearle and Nusslein-Volhard, 1987)
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\prd 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) prd-RA FBtr0080299  NM_078832   2328   590 prd-RB FBtr0080298  NM_164990   2422   613
Additional Transcript Data & Comments
Reported size (kB)	3.6, 2.5 (northern blot) (Kilchherr et al., 1986)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein prd-PA   FBpp0079883   62.9   590   7.46     NP_523556   AAF53160 prd-PB   FBpp0079882   65.5   613   7.47     NP_723721   AAN10801
Additional Polypeptide Data & Comments
Reported size (kDa)	613 (aa) (Frigerio et al., 1986)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeobox (IPR001356) Paired box protein, N-terminal (IPR001523) Homeodomain-like (IPR009057) Winged helix-turn-helix transcription repressor DNA-binding (IPR011991) Homeodomain-related (IPR012287) PDB - Protein Data Bank. An information portal to biological macromolecular structures • 1FJL 1PDN
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014134 AAF53160   AE014134 AAN10801   AI403282   AW941849   AY059447 AAL13353   BI590561   BI611788   BI624488   BI634555   CO329338   EC067321   EL870750   EL870751   ES690628   GH941793   GH943256   GH947677   GH949200   GH959496   GH961071   GH962436   GH968216   GH980128   K03518 CAB23650   K03519 CAB23651   M14548 AAB59221   Z71065
UniProtKB/Swiss-Prot	P06601
UniProtKB/TrEMBL
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
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference embryonic stage 4   organism | segment polarity expression pattern   (Kilchherr et al., 1986) embryonic stage 5   organism | segment polarity expression pattern   (Kilchherr et al., 1986) expression microarray Stage Tissue/Position (including subcellular localization) Reference adult stage | male     (Arbeitman et al., 2004) in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage     (Manoukian and Krause, 1992) epithelial cell   • cytoplasm | apical (Lecuyer et al., 2007) Comment:diffuse apical distribution epithelium   • cytoplasm | apical (Lecuyer et al., 2007) embryonic stage 6 -- 8   organism | segment polarity expression pattern   (Nasiadka and Krause, 1999) adult stage | male   testis   (Arbeitman et al., 2004) male accessory gland   (Arbeitman et al., 2004) adult stage | female   fat body | subset   (Arbeitman et al., 2004) Comment:expressed in female fat tissue surrounding the spermothecae
Additional Descriptive Data
	A 3.6kb prd transcript is observed in addition to the 2.5kb transcript in 0-4hr embryo RNA from prd4 heterozygous mothers. (Kilchherr et al., 1986) prd transcription is repressed by ectopic eve protein in evehs.PS embryos. Timing suggests that eve is a direct regulator of prd. (Manoukian and Krause, 1992) prd expression is enriched in adult males. (Arbeitman et al., 2004) prd transcripts rise to a sharp peak in 2-4 hr embryos, rapidly decline and are undetectable after 12 hrs. They are absent in oocytes. prd is initially expressed with double segment periodicity (7 stripes) but switches at cellular blastoderm to a pattern of single segment periodicity (14 stripes). (Kilchherr et al., 1986)
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage | early   organism | 60-80% egg length   (Gutjahr et al., 1994) Comment:62-75% egg length organism | odd pair rule expression pattern   (Gutjahr et al., 1994) embryonic stage 4 -- 5   organism | anterior & dorsal   (Gutjahr et al., 1994) embryonic stage 7 -- 8   organism | segment polarity expression pattern   (Gutjahr et al., 1994) embryonic stage 11   embryonic labral segment   (Gutjahr et al., 1994) embryonic labial segment   (Gutjahr et al., 1994) embryonic mandibular segment   (Gutjahr et al., 1994) embryonic maxillary segment   (Gutjahr et al., 1994) embryonic stage 12 -- 17   presumptive embryonic/larval central nervous system | restricted   (Gutjahr et al., 1994) adult stage | male   male accessory gland secondary cell   (Xue and Noll, 2002) male accessory gland main cell   (Xue and Noll, 2002)
Additional Descriptive Data
	prd protein is expressed in male accessory glands. It is initially expressed at high levels in all accessory gland cells, but protein levels decline with increasing age of virgin males. prd protein levels decline more rapidly in the main cells than in the secondary cells. In 10 day males, prd protein is detected only in scattered secondary cells in the distal region of the glands. Mating increases prd protein level s in both main and secondary cells throughout the glands. (Xue and Noll, 2002) prd protein is first detected in the anterior region of very early embryos and is subsequently restricted to a very narrow anterior stripe. During cellularization, bell-shaped stripes (stripes 3-7) are observed. The order of stripe appearance is 4 and 7, followed by 3 and 6, and finally stripe 5 emerges. At this point the anterior stripe splits into two. By mid-cellularization prd protein has reached equal levels in all stripes. At the same time, the preferential accumulation of prd protein at the posterior margins generates a gradient within each stripe. During the second half of cellularization, expression also occurs in a patch of cells at the anterior dorsal end of the embryo and in an eighth stripe. By the end of gastrulation, the number of stripes has doubled to 14 as a result of reduction of protein in the middle of the stripes accompanied by an increase of protein in the anterior region of the stripes. At the end of the germ band extended stage, the expression in the stripes has disappeared. prd protein is expressed in the head region, most strongly in the maxillary lobe, but also in the labial and mandibular lobes and in the clypeolabrum. prd protein is also detected in the developing CNS in 2-3 specific neurons per hemisegment. (Gutjahr et al., 1994)
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 FBgn0003145    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0003145 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 no expression detected. Peak expression observed within 00-06 hour embryonic stages, in adult male 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 FBgn0003145 expression level Developmental Stage   Expression Level embryo 00-02hr    125 embryo 02-04hr    3459 embryo 04-06hr    778 embryo 06-08hr    266 embryo 08-10hr    242 embryo 10-12hr    125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr    146 white prepupae 24hr    241 pupae 2d postWPP    254 pupae 3d postWPP    248 pupae 4d postWPP    521 adult male 01day    977 adult male 05day    1538 adult male 30day    2020 adult female 01day    9 adult female 05day    7 adult female 30day    3 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  (125) embryo 02-04hr  (3459) embryo 04-06hr  (778) embryo 06-08hr  (266) embryo 08-10hr  (242) embryo 10-12hr  (125) embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr  (146) white prepupae 24hr  (241) pupae 2d postWPP  (254) pupae 3d postWPP  (248) pupae 4d postWPP  (521) adult male 01day  (977) adult male 05day  (1538) adult male 30day  (2020) adult female 01day    9 adult female 05day    7 adult female 30day    3 Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    125 embryo 02-04hr  (3459) embryo 04-06hr    778 embryo 06-08hr    266 embryo 08-10hr    242 embryo 10-12hr    125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr    146 white prepupae 24hr    241 pupae 2d postWPP    254 pupae 3d postWPP    248 pupae 4d postWPP    521 adult male 01day    977 adult male 05day  (1538) adult male 30day  (2020) adult female 01day    9 adult female 05day    7 adult female 30day    3 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    125 embryo 02-04hr    3459 embryo 04-06hr    778 embryo 06-08hr    266 embryo 08-10hr    242 embryo 10-12hr    125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr    146 white prepupae 24hr    241 pupae 2d postWPP    254 pupae 3d postWPP    248 pupae 4d postWPP    521 adult male 01day    977 adult male 05day    1538 adult male 30day    2020 adult female 01day    9 adult female 05day    7 adult female 30day    3 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    125 embryo 02-04hr    3459 embryo 04-06hr    778 embryo 06-08hr    266 embryo 08-10hr    242 embryo 10-12hr    125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr    146 white prepupae 24hr    241 pupae 2d postWPP    254 pupae 3d postWPP    248 pupae 4d postWPP    521 adult male 01day    977 adult male 05day    1538 adult male 30day    2020 adult female 01day    9 adult female 05day    7 adult female 30day    3 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0003145 expression level Developmental Stage   Expression Level embryo 00-02hr    125 embryo 02-04hr    3459 embryo 04-06hr    778 embryo 06-08hr    266 embryo 08-10hr    242 embryo 10-12hr    125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr    146 white prepupae 24hr    241 pupae 2d postWPP    254 pupae 3d postWPP    248 pupae 4d postWPP    521 adult male 01day    977 adult male 05day    1538 adult male 30day    2020 adult female 01day    9 adult female 05day    7 adult female 30day    3 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  125 embryo 02-04hr  (3459) embryo 04-06hr  (778) embryo 06-08hr  (266) embryo 08-10hr  (242) embryo 10-12hr  125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr  (146) white prepupae 24hr  (241) pupae 2d postWPP  (254) pupae 3d postWPP  (248) pupae 4d postWPP  (521) adult male 01day  (977) adult male 05day  (1538) adult male 30day  (2020) adult female 01day    9 adult female 05day    7 adult female 30day    3 Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    125 embryo 02-04hr  (3459) embryo 04-06hr    778 embryo 06-08hr    266 embryo 08-10hr    242 embryo 10-12hr    125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr    146 white prepupae 24hr    241 pupae 2d postWPP    254 pupae 3d postWPP    248 pupae 4d postWPP    521 adult male 01day    977 adult male 05day  1538 adult male 30day  2020 adult female 01day    9 adult female 05day    7 adult female 30day    3 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    125 embryo 02-04hr    3459 embryo 04-06hr    778 embryo 06-08hr    266 embryo 08-10hr    242 embryo 10-12hr    125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr    146 white prepupae 24hr    241 pupae 2d postWPP    254 pupae 3d postWPP    248 pupae 4d postWPP    521 adult male 01day    977 adult male 05day    1538 adult male 30day    2020 adult female 01day    9 adult female 05day    7 adult female 30day    3 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    125 embryo 02-04hr    3459 embryo 04-06hr    778 embryo 06-08hr    266 embryo 08-10hr    242 embryo 10-12hr    125 embryo 12-14hr    93 embryo 14-16hr    67 embryo 16-18hr    41 embryo 18-20hr    58 embryo 20-22hr    41 embryo 22-24hr    45 larva L1    14 larva L2    7 larva L3 12hr old    0 larva L3 puffstage 1-2    41 larva L3 puffstage 3-6    81 larva L3 puffstage 7-9    92 white prepupae new    75 white prepupae 12hr    146 white prepupae 24hr    241 pupae 2d postWPP    254 pupae 3d postWPP    248 pupae 4d postWPP    521 adult male 01day    977 adult male 05day    1538 adult male 30day    2020 adult female 01day    9 adult female 05day    7 adult female 30day    3 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 FBgn0003145    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0003145 Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: 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 FBgn0003145 expression level Tissue   Expression Level Larval Central Nervous System    7.65 Larval Midgut    4.9 Larval Hindgut    4.8 Larval Malpighian Tubules    4.6 Larval Fat Body no informative data Larval Salivary Gland    9.9 Larval Trachea    0.55 Larval Carcass    1.525 Adult Head    5.7 Adult Eye    2.025 Adult Brain    1.9 Adult Thoracic-Abdominal Ganglion    3.5 Adult Crop    5.9 Adult Midgut    3 Adult Hindgut    3.6 Adult Malpighian Tubules    5 Adult Fat Body no informative data Adult Salivary Gland    9.8 Adult Heart    2.15 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data Adult Ovary    3.7 Adult Testis    25.2 Adult Male Accessory Gland    3050.9 Adult Carcass    9.2 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    7.65 Larval Midgut    4.9 Larval Hindgut    4.8 Larval Malpighian Tubules    4.6 Larval Fat Body no informative data Larval Salivary Gland    9.9 Larval Trachea    0.55 Larval Carcass    1.525 Adult Head    5.7 Adult Eye    2.025 Adult Brain    1.9 Adult Thoracic-Abdominal Ganglion    3.5 Adult Crop    5.9 Adult Midgut    3 Adult Hindgut    3.6 Adult Malpighian Tubules    5 Adult Fat Body no informative data Adult Salivary Gland    9.8 Adult Heart    2.15 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data Adult Ovary    3.7 Adult Testis    25.2 Adult Male Accessory Gland  (3050.9) Adult Carcass    9.2 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    7.65 Larval Midgut    4.9 Larval Hindgut    4.8 Larval Malpighian Tubules    4.6 Larval Fat Body no informative data Larval Salivary Gland    9.9 Larval Trachea    0.55 Larval Carcass    1.525 Adult Head    5.7 Adult Eye    2.025 Adult Brain    1.9 Adult Thoracic-Abdominal Ganglion    3.5 Adult Crop    5.9 Adult Midgut    3 Adult Hindgut    3.6 Adult Malpighian Tubules    5 Adult Fat Body no informative data Adult Salivary Gland    9.8 Adult Heart    2.15 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data Adult Ovary    3.7 Adult Testis    25.2 Adult Male Accessory Gland  (3050.9) Adult Carcass    9.2 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    7.65 Larval Midgut    4.9 Larval Hindgut    4.8 Larval Malpighian Tubules    4.6 Larval Fat Body no informative data Larval Salivary Gland    9.9 Larval Trachea    0.55 Larval Carcass    1.525 Adult Head    5.7 Adult Eye    2.025 Adult Brain    1.9 Adult Thoracic-Abdominal Ganglion    3.5 Adult Crop    5.9 Adult Midgut    3 Adult Hindgut    3.6 Adult Malpighian Tubules    5 Adult Fat Body no informative data Adult Salivary Gland    9.8 Adult Heart    2.15 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data Adult Ovary    3.7 Adult Testis    25.2 Adult Male Accessory Gland    3050.9 Adult Carcass    9.2 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0003145 expression level Tissue   Expression Level Larval Central Nervous System    7.65 Larval Midgut    4.9 Larval Hindgut    4.8 Larval Malpighian Tubules    4.6 Larval Fat Body no informative data Larval Salivary Gland    9.9 Larval Trachea    0.55 Larval Carcass    1.525 Adult Head    5.7 Adult Eye    2.025 Adult Brain    1.9 Adult Thoracic-Abdominal Ganglion    3.5 Adult Crop    5.9 Adult Midgut    3 Adult Hindgut    3.6 Adult Malpighian Tubules    5 Adult Fat Body no informative data Adult Salivary Gland    9.8 Adult Heart    2.15 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data Adult Ovary    3.7 Adult Testis    25.2 Adult Male Accessory Gland    3050.9 Adult Carcass    9.2 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    7.65 Larval Midgut    4.9 Larval Hindgut    4.8 Larval Malpighian Tubules    4.6 Larval Fat Body no informative data Larval Salivary Gland    9.9 Larval Trachea    0.55 Larval Carcass    1.525 Adult Head    5.7 Adult Eye    2.025 Adult Brain    1.9 Adult Thoracic-Abdominal Ganglion    3.5 Adult Crop    5.9 Adult Midgut    3 Adult Hindgut    3.6 Adult Malpighian Tubules    5 Adult Fat Body no informative data Adult Salivary Gland    9.8 Adult Heart    2.15 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data Adult Ovary    3.7 Adult Testis    25.2 Adult Male Accessory Gland  (3050.9) Adult Carcass    9.2 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    7.65 Larval Midgut    4.9 Larval Hindgut    4.8 Larval Malpighian Tubules    4.6 Larval Fat Body no informative data Larval Salivary Gland    9.9 Larval Trachea    0.55 Larval Carcass    1.525 Adult Head    5.7 Adult Eye    2.025 Adult Brain    1.9 Adult Thoracic-Abdominal Ganglion    3.5 Adult Crop    5.9 Adult Midgut    3 Adult Hindgut    3.6 Adult Malpighian Tubules    5 Adult Fat Body no informative data Adult Salivary Gland    9.8 Adult Heart    2.15 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data Adult Ovary    3.7 Adult Testis    25.2 Adult Male Accessory Gland  (3050.9) Adult Carcass    9.2 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    7.65 Larval Midgut    4.9 Larval Hindgut    4.8 Larval Malpighian Tubules    4.6 Larval Fat Body no informative data Larval Salivary Gland    9.9 Larval Trachea    0.55 Larval Carcass    1.525 Adult Head    5.7 Adult Eye    2.025 Adult Brain    1.9 Adult Thoracic-Abdominal Ganglion    3.5 Adult Crop    5.9 Adult Midgut    3 Adult Hindgut    3.6 Adult Malpighian Tubules    5 Adult Fat Body no informative data Adult Salivary Gland    9.8 Adult Heart    2.15 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data Adult Ovary    3.7 Adult Testis    25.2 Adult Male Accessory Gland    3050.9 Adult Carcass    9.2 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 no informative data 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 no informative data Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca no informative data 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    5.7   NA  Eye    2.025   NA  Brain    1.9   7.65  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    3.5   NA  Crop    5.9   4.9  Midgut    3   4.8  Hindgut    3.6   4.6  Malpighian Tubules    5   no informative data  Fat Body    no informative data   9.9  Salivary Gland    9.8   NA  Heart    2.15   0.55  Trachea    NA   NA  VirginFemale Spermatheca    no informative data   NA  InseminatedFemale Spermatheca    no informative data   NA  Ovary    3.7   NA  Testis    25.2   NA  Male Accessory Gland    3050.9   1.525  Carcass    9.2 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_21
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003145 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG6716-RB FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for prd Stages(s) 1-3 Stages(s) 4-6 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal prdN lethal | embryonic stage | pair rule expression pattern | recessive prdunspecified lethal | embryonic stage | recessive prd4 lethal | heat sensitive prd10 semi-lethal | pupal stage, with Scer\GAL4pnr-MD237 prdGD1505 Sterility Allele male sterile prd4 male sterile, with Df(2L)Prl/prd4 prdwt male sterile (with Df(2L)Prl), with prdwt prd4 Other Phenotypes Allele visible, with Scer\GAL4ey.PH prdScer\UAS.cJa wild-type prd+mXa prd+t18 prdmf5 prdmf7 prdmf8 prdmf9 prdwt prdΔPR.hs prdΔPRD Phenotype manifest in Allele abdomen & cuticle & adult prdwt abdominal 2 ventral denticle belt prdunspecified abdominal 2 ventral denticle belt | embryonic stage | pair rule expression pattern prdhs.PL abdominal 4 ventral denticle belt prdunspecified abdominal 4 ventral denticle belt | embryonic stage | pair rule expression pattern prdhs.PL abdominal 6 ventral denticle belt prdunspecified abdominal 6 ventral denticle belt | embryonic stage | pair rule expression pattern prdhs.PL abdominal 8 ventral denticle belt | embryonic stage | pair rule expression pattern prdhs.PL adult head, with Scer\GAL4ey.PH prdScer\UAS.cJa antenna, with Scer\GAL4ey.PH prdScer\UAS.cJa cephalic furrow prdunspecified cuticle prdΔPB.hs denticle belt prd9 prdhs.PM denticle belt | larval stage prd8 EL neuron prdhs.PL embryonic/first instar larval cuticle & abdominal segment 1 prdunspecified embryonic/first instar larval cuticle & abdominal segment 3 prdunspecified embryonic/first instar larval cuticle & abdominal segment 5 prdunspecified embryonic/first instar larval cuticle & abdominal segment 7 prdunspecified embryonic/first instar larval cuticle & mesothoracic segment prdunspecified embryonic/larval cuticle prd8 embryonic abdominal segment 1 & cardioblast prddsRNA.cKa embryonic abdominal segment 1 & muscle founder cell prddsRNA.cKa embryonic abdominal segment 3 & cardioblast prddsRNA.cKa embryonic abdominal segment 3 & muscle founder cell prddsRNA.cKa embryonic labial segment prd9 eye, with Scer\GAL4ey.PH prdScer\UAS.cJa heart primordium prddsRNA.cKa prddsRNA.si.cKa larval midgut & embryo & epidermis prd6 male accessory gland prd4 prdwt male accessory gland, with Df(2L)Prl/prd4 prdwt male accessory gland (with Df(2L)Prl), with prdwt prd4 metathoracic ventral denticle belt prdunspecified prothoracic ventral denticle belt prdunspecified RP2 neuron prdhs.PL syncytial blastoderm embryo prdunspecified U neuron prdhs.PL
Classical Alleles ( 15 )
For All Classical Alleles Show
Allele of prd Class Mutagen Stocks Known lesion prd9 ethyl methanesulfonate 14 -- prd8 hypomorphic allele - genetic evidence ethyl methanesulfonate 2 -- prd4 amorphic allele - genetic evidence X ray 1 Yes prd12 antimorphic allele - genetic evidence X ray 1 Yes prd7 X ray 1 -- prd10 ethyl methanesulfonate 0 Yes prd11 ethyl methanesulfonate 0 -- prd1 ethyl methanesulfonate 0 -- prd2 ethyl methanesulfonate 0 -- prd2N47 0 -- prd3 X ray 0 -- prd5 X ray 0 -- prd6 ethyl methanesulfonate 0 -- prdF121 0 -- prdunspecified 0 --
Alleles Carried on Transgenic Constructs ( 58 )
For All Alleles Carried on Transgenic Constructs Show
Allele of prd Class Mutagen Stocks Known lesion prdGD1505 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes prdHMS00922 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes prd+mXa in vitro construct - deletion 0 Yes prd+t18 in vitro construct - genomic fragment 0 Yes prd3'2.Act5C in vitro construct - deletion 0 Yes prd3'3.Act5C in vitro construct - deletion 0 Yes prd3'4.Act5C in vitro construct - deletion 0 Yes prd3'5.Act5C in vitro construct - deletion 0 Yes prd3'6.Act5C in vitro construct - deletion 0 Yes prd5'1.Act5C in vitro construct - deletion 0 Yes prd5'2.Act5C in vitro construct - deletion 0 Yes prd5'3.Act5C in vitro construct - deletion 0 Yes prd5'4.Act5C in vitro construct - deletion 0 Yes prd5'5.Act5C in vitro construct - deletion 0 Yes prd539-572.T:Mmmm\Sp1 in vitro construct - coding region fusion 0 Yes prd539-613.T:Mmmm\Sp1 in vitro construct - coding region fusion 0 Yes prd573-613.T:Mmmm\Sp1 in vitro construct - coding region fusion 0 Yes prdAct5C.PH in vitro construct - regulatory fusion 0 Yes prdAR in vitro construct - site directed mutagenesis 0 Yes prdcBa in vitro construct 0 -- prddsRNA.cKa in vitro construct - RNAi 0 Yes prddsRNA.si.cKa in vitro construct - RNAi 0 Yes prdGS in vitro construct - site directed mutagenesis 0 Yes prdgsb.PL in vitro construct - regulatory fusion 0 Yes prdhs.P1-1 in vitro construct - regulatory fusion 0 Yes prdhs.PL gain of function allele in vitro construct - regulatory fusion 0 Yes prdhs.PM in vitro construct - regulatory fusion 0 Yes prdIWF in vitro construct 0 Yes prdK9.hs in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes prdmf10 in vitro construct 0 Yes prdmf1 in vitro construct - deletion 0 Yes prdmf2 in vitro construct - deletion 0 Yes prdmf3 in vitro construct - deletion 0 Yes prdmf4 in vitro construct - deletion 0 Yes prdmf5 in vitro construct 0 Yes prdmf7 in vitro construct 0 Yes prdmf8 in vitro construct 0 Yes prdmf9 in vitro construct 0 Yes prdN in vitro construct - deletion 0 Yes prdNQ in vitro construct - site directed mutagenesis 0 Yes prdO.hs in vitro construct - regulatory fusion in vitro construct 0 Yes prdQ9.hs in vitro construct - regulatory fusion in vitro construct - amino acid replacement 0 Yes prdQ9Q10.hs in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes prdRev.hs in vitro construct - regulatory fusion 0 Yes prdScer\UAS.cJa in vitro construct - regulatory fusion 0 Yes prdSQ in vitro construct - site directed mutagenesis 0 Yes prdun.hs in vitro construct - site directed mutagenesis in vitro construct - amino acid replacement in vitro construct - regulatory fusion 0 Yes prdWT.Act5C in vitro construct - regulatory fusion 0 Yes prdwt hypomorphic allele - genetic evidence in vitro construct 0 Yes prdΔ1.Act5C in vitro construct - deletion in vitro construct - regulatory fusion 0 Yes prdΔHD.hs in vitro construct - deletion 0 Yes prdΔPB.hs in vitro construct - deletion 0 Yes prdΔPBC.hs in vitro construct - deletion 0 Yes prdΔPBN.hs in vitro construct - deletion 0 Yes prdΔPR.hs in vitro construct 0 Yes prdΔPRD in vitro construct - deletion 0 Yes prdΔPRt.hs in vitro construct - amino acid replacement in vitro construct - site directed mutagenesis 0 Yes prdΔPRT in vitro construct - deletion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2L)BSC826 (Christensen et al., 2009.7.22) Df(2L)BSC891 (Cook and Cook, 2010.10.13) Df(2L)esc-P3-0 (Jurgens, 1988, Harbecke and Lengyel, 1995) Df(2L)Exel6032 (Ryder, 2004.4.26) Df(2L)prd (Muller et al., 1999, Jurgens, 1988) Df(2L)prd1.7 (Jurgens, 1988, Harbecke and Lengyel, 1995, Yeo et al., 1995) Df(2L)prd1.25 (Nusslein-Volhard et al., 1985, Tearle and Nusslein-Volhard, 1987, van den Heuvel et al., 1993) Df(2L)prd2.27 (Muller et al., 1999) Df(2L)Prl (Nusslein-Volhard et al., 1984, Jurgens, 1988, Harbecke and Lengyel, 1995, Yeo et al., 1995)
Duplicated in	Dp(2;2)GYL (Jurgens, 1988) Dp(2;Y)prd (Jurgens, 1988)
Not disrupted in	Df(2L)esc10 (Jurgens, 1988) Df(2L)esc-P2-0 (Jurgens, 1988) Df(2L)esc-P2-0+Dp(2;2)GYL (Jurgens, 1988) Df(2L)GR4 (Yeo et al., 1995) Df(2L)prd+Dp(2;2)GYL (Jurgens, 1988) Df(2L)Prl+Dp(2;2)GYL (Jurgens, 1988)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data reporter construct P{PH0-lacZ} No P{prd-lacZ.CRM} No P{prdΔC} No P{prdΔD} No P{prdΔE} No P{prdΔF} No P{prdΔG} No P{prdΔH} No P{prdΔI} No P{prdΔK} No P{prdΔL} No P{prdΔM} No P{prdΔN} No P{prdΔO} No P{prdΔP} No P{prdΔQ} No P{XPDNP-lacZ} No heat-shock construct P{hs1-1} NA P{hs-prd.K9} NA P{Hs-prd.L} NA P{hs-prd.M} NA P{hs-prd.Q9} NA P{hs-prd.Rev} NA P{hs-prdQ9Q10} NA P{hs-prdun} NA P{hs-prdΔPB} NA P{hs-prdΔPBC} NA P{hs-prdΔPBN} NA P{hs-prdΔPR} NA P{hs-prdΔPRt} NA UAS construct P{GD1505} NA P{TRiP.HMS00922} NA P{UAS-prd.J} NA characterization construct P{gsb-prd} NA P{hs-ftz::prd.PFP} NA P{hs-ftz/prdHD/ftz} NA P{hs-prd::Mmus\Pax8.L} NA P{P2-lacZ} NA P{prd+mXa} NA P{prdN} NA P{prdt.Res} NA P{prdΔPRD} NA P{prdAR} NA P{prd-GAL4.3.1} NA P{prdGS} NA P{prd-gsb.+PRD} NA P{prd-GsbN+PrdC} NA P{prd-mf1.GAL4} NA P{prd-mf2.GAL4} NA P{prd-mf3.GAL4} NA P{prd-mf4.GAL4} NA P{prd-mf5.GAL4} NA P{prd-mf7.GAL4} NA P{prd-mf8.GAL4} NA P{prd-mf9.GAL4} NA P{prd-mf10.GAL4} NA P{prdNQ} NA P{prd-Pax3} NA P{prd-PrdN-GsbC} NA P{prd-SN20} NA P{prdSQ} NA P{prdwt} NA P{prdΔPBC} NA P{prdΔPR} NA P{prdΔPRT} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 9 unique terms )
Terms Based on Experimental Evidence ( 3 terms )
Molecular Function
CV term Evidence References
RNA polymerase II regulatory region sequence-specific DNA binding inferred from direct assay (Li and Noll, 1994) sequence-specific distal enhancer binding RNA polymerase II transcription factor activity inferred from direct assay (Bouchard et al., 2000)
Biological Process
CV term Evidence References
positive regulation of transcription from RNA polymerase II promoter inferred from direct assay (Bouchard et al., 2000)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 6 terms )
Molecular Function
CV term Evidence References
DNA binding non-traceable author statement (Swiss-Prot Project Members, 1988.1.1) sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with mouse Pax3 (FlyBase, 1992-)
Biological Process
CV term Evidence References
periodic partitioning by pair rule gene non-traceable author statement (Swiss-Prot Project Members, 1988.1.1, Davis and Patel, 2003) traceable author statement (Peel, 2004) regulation of transcription, DNA-dependent inferred from sequence or structural similarity with mouse Pax3 (FlyBase, 1992-)
Cellular Component
CV term Evidence References
nucleus non-traceable author statement (Swiss-Prot Project Members, 1988.1.1) transcription factor complex inferred from sequence or structural similarity with mouse Pax3 (FlyBase, 1992-)
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 prd allele Gene References prd4 gsb (Xue et al., 2001, Xue and Noll, 2002) gsb::prd (Xue et al., 2001) h (Bianchi-Frias et al., 2004) prdmf5 gsb (Xue and Noll, 2002) prdScer\UAS.cJa CycE (Jiao et al., 2001) dm (Jiao et al., 2001) unspecified RpII140 (Parkhurst and Ish-Horowicz, 1991)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 60680 DroID - A comprehensive database of gene and protein interactions. • FBgn0003145 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 34629
Orthologs
Genome-wide drosophilid orthologs	Dana\GF23439 Dere\GG10275 Dgri\GH10195 Dmoj\GI14821 Dper\GL14130 Dpse\GA19807 Dsec\GM26340 Dsim\GD22133 Dvir\GJ23973 Dwil\GK21081 Dyak\GE12435
Curated drosophilid orthologs	Dmau\prd   Dpse\GA19807   Dsim\prd   Dwil\prd (Matsuo, 1996)
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • XP_001949018.1 Acyrthosiphon pisum (pea aphid) ENSBTAP00000013131 Bos taurus (bovine) ENSCAFP00000022903 Canis familiaris (dog) ENSCAFP00000023626 Canis familiaris (dog) ENSCINP00000018028 Ciona intestinalis (sea squirt) ENSCPOP00000005658 Cavia porcellus (guinea pig) ENSCSAVP00000008050 Ciona savignyi (sedentary tunicate) 64892 Capitella spl (polychaete worm) DEHA2F22286g Debaryomyces Hansenii (yeast) 265088 Daphnia pulex (daphnia) ENSDARP00000022138 Danio rerio (zebra fish) ENSECAP00000012896 Equus caballus (horse) ENSGACP00000017071 Gymnopilus aculeatus (mushroom) ENSGALP00000005992 Gallus gallus (chicken) ENSP00000343052 Homo sapiens (human) ENSMODP00000026484 Monodelphis domestica (gray opossum) ENSMMUP00000026853 Macaca mulatta (rhesus monkey) ENSMUSP00000030508 Mus musculus (house mouse) ENSORLP00000005345 Oryzias latipes (japanese killifish) ENSPPYP00000014772 Pongo pygmaeus (orangutan) ENSPTRP00000022161 Pan troglodytes (chimpanzee) ENSRNOP00000025488 Rattus norvegicus (norway rat) NP_001071090.1 Tribolium castaneum (red flour beetle) ENSTNIP00000017836 Tetraodon nigroviridis (green spotted pufferfish) ENSTRUP00000034277 Takifugu rubripes (pufferfish Takifugu) ENSXETP00000040102 Xenopus tropicalis (frog) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • PB18089 PB12792 NV18360 LH15339 LH16584 LH16582 ISCW014979 FBgn0232069 FBgn0230178 FBgn0229199 FBgn0223712 FBgn0223568 FBgn0223073 FBgn0211060 FBgn0208469 FBgn0208157 FBgn0196214 FBgn0193543 FBgn0183657 FBgn0181193 FBgn0166863 FBgn0166708 JGI_V11_7942 JGI_V11_45999 JGI_V11_334067 FBgn0079803 FBgn0077432 FBgn0075449 FBgn0155247 FBgn0154435 FBgn0151735 FBgn0143898 FBgn0141217 FBgn0001148 FBgn0001147 FBgn0130594 FBgn0130115 FBgn0115188 FBgn0112065 FBgn0102584 FBgn0100433 FBgn0090393 FBgn0088552 CPIJ006496 BGIBMGA009025 ACYPI004907 ACYPI002777 GB15632 GB15469 AGAP010358 PHUM134580 PHUM375940 GLEAN_06788 GLEAN_05342 GLEAN_15804
Stocks & Reagents
Stocks Listed in FlyBase ( 21 )
Bloomington	5806 prd8/CyO 34506 prd12 b1 pr1/CyO 5346 w*; prd9/CyO; P{ftz/lacC}1 1598 prd9 cn1 bw1 sp1/CyO 3692 odd5 prd9 c1 px1 sp1/SM6a 2256 slp11 prd9 c1 px1 sp1/SM6a 3305 odd5 dpov1 prd9 cn1 eve1/CyO
Kyoto	108434 prd8/CyO 106408 prd9 cn1 bw1 sp1/CyO 106969 odd5 dpov1 prd9 cn1 eve1/CyO 101409 CyO, Cy1 dplv1 pr1 cn2 / prd7
VDRC	v6221 w1118; P{GD1505}v6221
	More stocks available...
Genomic Clones ( 1 )
	BACR02B06 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 17 )
	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	GH22686
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RH04201 RH18194 RH38735 RH64053
Other clones	190323 EK292631 IP02821 RP004188867 RP004205895 RP004243314 RP004253133 RP004262782 RP004457888 RP004525444 RP004539124 RP004557555
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0003145 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 34629
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: prd CG6716 (Zhong, 1999.11)
Source for database merge of
Additional comments
Other Comments
	prd is required for promoting cell proliferation during early accessory gland development. (Xue and Noll, 2002) In embryos, prd and bcd gene products bind most strongly to known target elements within a promoter. In addition, they may also bind at significant levels to the majority of genes, as do the selector homeoproteins. (Carr and Biggin, 1999) In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes. (Kliman and Eyre-Walker, 1998) Ecol\CAT assays in culture cells reveal both the prd domain (PD) and the homeodomain (HD) can mediate transcriptional activation independently. PD binding sites are able to mimic the expression pattern of prd in vivo. In vivo expression of a PD reporter gene only requires prd to bind through its PD. Different C-terminal regions are involved in transactivation mediated by the HD or the PD. (Sheng et al., 1997) Both the HD and the N-terminal subdomain of the PD (the PAI domain) are absolutely required within the same molecule for normal prd function. The conserved C-terminal subdomain of the PD (RED domain) appears to be dispensable. Inability to dimerize via the HD reduces but does not abolish the ability of the prd product to function. Deletion of the PRD repeat reduces but does not abolish the ability of the prd product to function. While prd can use its DNA-binding domains combinatorially in order to achieve different DNA-binding specificities, its principal binding mode requires a cooperative interaction between the PAI domain and the homeodomain. (Bertuccioli et al., 1996) ftz protein lacking the homeodomain can directly regulate ftz-dependent segmentation, suggesting that it can control target gene expression through interactions with other proteins. A likely candidate is the pair-rule protein prd. (Copeland et al., 1996) prd regulates late even skipped expression through a composite binding site for the paired domain and the homeodomain. Mutagenesis of either binding site leads to significant reduction in the activity of the late element, indicating that both domains are required for regulation. (Fujioka et al., 1996) Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire. The prd protein can bind, in vitro, exclusively through its PAI domain, or through a dimer of its HD, or through cooperative interaction between the PAI domain and HD. However, prd function in vivo requires the synergistic action of both the PAI domain and the HD. (Jun and Desplan, 1996) Both the paired domain and the homeodomain are required for in vivo function of the prd protein. (Miskiewicz et al., 1996) gsb and prd show functional equivalence; gsb is able to substitute for all functions of prd required to support development to adults. Mmus\Pax3 protein cannot substitute for all prd functions. (Xue and Noll, 1996) The PRD-repeat domains of slou and prd protein are sufficient to mediate protein-protein interaction, suggesting that the PRD-domain functions as a protein-binding interface and thereby may increase the DNA binding specificity of homeodomain transcription factors. (Kim et al., 1995) wg expression is regulated by odd and prd. odd represses wg expression, prd restricts the domain of expression of odd. (Mullen and DiNardo, 1995) Induction of anti-prd ribozymes specifically reduces prd protein levels. Induction of the ribozymes at late stages does not affect embryonic segmentation but leads to specific defects in head structures. (Vanario-Alonso et al., 1995) The paired domain of the prd protein has been crystallised and its structure solved. The structure reveals how a β turn can be used for minor groove recognition, provides new information about the docking of a helix turn helix units and provides a structural basis for the understanding of PAX developmental mutants. (Xu et al., 1995) The prd repeat is not required for the in vivo regulation of the target genes en and gsb. The prd repeat appears to be embedded within a Pro-rich transcriptional activation domain required for the regulation of these genes. Analysis of the prd domain indicates the N-terminal half, which is required for DNA binding in vitro, is also required for in vivo function, whereas the C-terminal half is dispensable for the regulation of en and gsb. (Cai et al., 1994) An 18kb genomic fragment consisting of the transcribed region and 10kb of 5' and 5kb of 3' flanking sequences is able to rescue prd mutant embryos to full viability. Regulation of prd by pair-rule and gap gene products is mediated by upstream and downstream cis-regulatory elements. (Gutjahr et al., 1994) Ectopic expression analysis demonstrates that the gsb and gsb-n gene product can substitute the function of the prd gene product during early embryonic development and prd gene product can substitute gsb and gsb-n gene product during late embryonic development in regulating expression of wg and en. (Li and Noll, 1994) Transient expression assays using Ecol\CAT reporter gene constructs have been used to define the sequences responsible for the synergistic action of ftz and prd, these have been mapped to different regions of the two proteins. ftz protein has a synergistic effect on transcription of a target promoter in the presence of prd protein that is apparently entirely independent of binding of ftz protein to the promoter DNA. This synergism is dependent on the presence of homeodomain DNA binding sites in the promoter and does not occur at active promoters that are not regulated by homeodomain. (Ananthan et al., 1993) Expression of prd depends on activation by gap gene hb, Kr, kni and gt products. Primary pair rule gene products act primarily in subsequent modulation rather than activation of prd stripes. Factors activating prd expression in the pair rule mode interact with those activating it along the dorso-ventral axis. (Gutjahr et al., 1993) wg expression is aberrantly activated and regulated in pair rule mutant embryos. (Ingham and Hidalgo, 1993) The role of prd in the regulation of run mRNA expression in the early embryo has been investigated. (Klingler and Gergen, 1993) Homeo domain cooperative dimerization, binding site configuration and binding site sequence specificity allow for distinction between homeo domain proteins within the prd domain. (Wilson et al., 1993) Expression of prd is repressed by ectopic expression of eve. (Manoukian and Krause, 1992) Mutant analysis shows that wild type prd function is required to set up expression of ac and sc in row B and D, respectively, of the embryonic proneural cluster. (Skeath et al., 1992) Mutations in zygotic pair rule gene prd interact with RpII140wimp. (Parkhurst and Ish-Horowicz, 1991) The paired box of prd encodes a DNA-binding activity, independent of the DNA-binding activity of the homeodomain and with a different sequence specificity. (Treisman et al., 1991) prd RNA expression during early embryogenesis has been studied in wild-type and single double pair-rule mutant embryos. The regulation of prd expression is subject to a regulatory hierarchy among the pair-rule genes, and prd is at the bottom of this hierarchy, mediating the transition from pair-rule to segment-polarity genes. The transition of prd expression from the early 'pair-rule' pattern to the 'segment-polarity' pattern is regulated by the secondary pair-rule genes opa and odd. (Baumgartner and Noll, 1990) A transient expression assay has been employed to investigate the potential of homeobox genes to function as transcriptional activators. (Han et al., 1989) Genetic analysis demonstrates that prd is dispensable for efficient homeotic gene expression in the visceral mesoderm. (Tremml and Bienz, 1989) The DNA binding activities of the en, eve, prd and zen proteins have been compared. (Hoey and Levine, 1988) The wild-type allele of prd is required for normal segmentation in embryos and larvae. Mutant alleles and deficiencies show no maternal effect in homozygous germ-line cloness and are embryonic lethals with half the normal number of segmental units. In strong mutants, the anterior part of segments T1, T3, A2, A4, A6 and A8 and the posterior part of T2, A1, A3, A5 and A7 (i.e., odd-numbered parasegments) are deleted (Nusslein-Volhard, Kluding and Jurgens, 1985). Weak mutants such as prd2 show small and less regular segmental deletions. Structures missing in prd mutants include: derivatives of the mandibular segments, labial sense organs, anterior prothorax, posterior mesothorax, anterior metathorax and alternating posterior and anterior abdominal segments, including the telson and the posterior lateral sense organs (Nusslein-Volhard, Kluding and Jurgens, 1985). No head fold visible at gastrulation. Experiments with a temperature-sensitive mutant indicate that the TSP occurs during the cellular blastoderm stage (Nusslein-Volhard et al., 1985; Kilchherr et al., 1986).
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_078832 NM_164990 RefSeq (Proteins) • NP_523556 NP_723721 DDBJ / EMBL / GenBank • AAB59221 AAF53160 AAF53160.1 AAL13353 AAN10801 AAN10801.1 AI403282 AW941849 AY059447 CAB23650 CAB23651 K03518 K03519 M14548 Z71065 Entrez Gene - A searchable database of RefSeq genes. • 34629 UniProtKB/Swiss-Prot • P06601
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeobox (IPR001356) Paired box protein, N-terminal (IPR001523) Homeodomain-like (IPR009057) Winged helix-turn-helix transcription repressor DNA-binding (IPR011991) Homeodomain-related (IPR012287) PDB - Protein Data Bank. An information portal to biological macromolecular structures • 1FJL 1PDN
Linkouts
	BioGRID - A database of protein and genetic interactions • 60680 DroID - A comprehensive database of gene and protein interactions. • FBgn0003145 DRSC - Results from RNAi screens. • FBgn0003145 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003145 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG6716-RB FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0003145 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 34629 InParanoid A subset of ortholog calls from InParanoid. • XP_001949018.1 Acyrthosiphon pisum (pea aphid) ENSBTAP00000013131 Bos taurus (bovine) ENSCAFP00000022903 Canis familiaris (dog) ENSCAFP00000023626 Canis familiaris (dog) ENSCINP00000018028 Ciona intestinalis (sea squirt) ENSCPOP00000005658 Cavia porcellus (guinea pig) ENSCSAVP00000008050 Ciona savignyi (sedentary tunicate) 64892 Capitella spl (polychaete worm) DEHA2F22286g Debaryomyces Hansenii (yeast) 265088 Daphnia pulex (daphnia) ENSDARP00000022138 Danio rerio (zebra fish) ENSECAP00000012896 Equus caballus (horse) ENSGACP00000017071 Gymnopilus aculeatus (mushroom) ENSGALP00000005992 Gallus gallus (chicken) ENSP00000343052 Homo sapiens (human) ENSMODP00000026484 Monodelphis domestica (gray opossum) ENSMMUP00000026853 Macaca mulatta (rhesus monkey) ENSMUSP00000030508 Mus musculus (house mouse) ENSORLP00000005345 Oryzias latipes (japanese killifish) ENSPPYP00000014772 Pongo pygmaeus (orangutan) ENSPTRP00000022161 Pan troglodytes (chimpanzee) ENSRNOP00000025488 Rattus norvegicus (norway rat) NP_001071090.1 Tribolium castaneum (red flour beetle) ENSTNIP00000017836 Tetraodon nigroviridis (green spotted pufferfish) ENSTRUP00000034277 Takifugu rubripes (pufferfish Takifugu) ENSXETP00000040102 Xenopus tropicalis (frog) Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /segment/paired.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 34629 modMine - Data generated by the modENCODE project. • FBgn0003145 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • PB18089 PB12792 NV18360 LH15339 LH16584 LH16582 ISCW014979 FBgn0232069 FBgn0230178 FBgn0229199 FBgn0223712 FBgn0223568 FBgn0223073 FBgn0211060 FBgn0208469 FBgn0208157 FBgn0196214 FBgn0193543 FBgn0183657 FBgn0181193 FBgn0166863 FBgn0166708 JGI_V11_7942 JGI_V11_45999 JGI_V11_334067 FBgn0079803 FBgn0077432 FBgn0075449 FBgn0155247 FBgn0154435 FBgn0151735 FBgn0143898 FBgn0141217 FBgn0001148 FBgn0001147 FBgn0130594 FBgn0130115 FBgn0115188 FBgn0112065 FBgn0102584 FBgn0100433 FBgn0090393 FBgn0088552 CPIJ006496 BGIBMGA009025 ACYPI004907 ACYPI002777 GB15632 GB15469 AGAP010358 PHUM134580 PHUM375940 GLEAN_06788 GLEAN_05342 GLEAN_15804 REDfly - A database of transcriptional regulatory elements. • FBgn0003145
Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym	CG6716 (Ni et al., 2010.12.1) pr (Ho, 1990) prd (Ravi Ram et al., 2005, Peel et al., 2005, Oakley et al., 2006, Sandmann et al., 2007, Segal et al., 2008, Hueber et al., 2007, Lecuyer et al., 2007, Goldstein et al., 2005, Baig-Lewis et al., 2007, Surkova et al., 2008, McKay et al., 2009, Ochoa-Espinosa et al., 2009, Christensen et al., 2009.7.22, Pisarev et al., 2009, Schaaf et al., 2009, Zhai et al., 2009, Sawamura and Yamamoto, 2004, Surkova et al., 2008, Luengo Hendriks et al., 2006, Grad et al., 2004, Cook and Cook, 2010.10.13, Zhang and Arnosti, 2011, Chatterjee et al., 2011, Friedrich and Caravas, 2011, Pruteanu-Malinici et al., 2011, Cunha et al., 2010, Kazemian et al., 2010, Tchuraev and Galimzyanov, 2009, Fowlkes et al., 2011) Prd (Vivekanand et al., 2001, Wilson et al., 1993, Treisman et al., 1991, Treisman et al., 1989, Davis et al., 2005, Qian et al., 2011, Noyes et al., 2008, Formstecher et al., 2005, The modENCODE Consortium, 2010, The modENCODE Consortium, 2010) PRD (MacArthur et al., 2009, modENCODE Consortium et al., 2010)
Name Synonym	paired (Hueber et al., 2007, Goldstein et al., 2005, Gregor et al., 2005, Ochoa-Espinosa et al., 2009, Pisarev et al., 2009, Zhai et al., 2009, Sawamura and Yamamoto, 2004, Surkova et al., 2008, Wilkie et al., 2001, Formstecher et al., 2005, Zamparo and Perkins, 2009, Chatterjee et al., 2011, Friedrich and Caravas, 2011) Paired (Veitia, 2006, Wheeler et al., 2006, Reig et al., 2007, Gregor et al., 2008, Noyes et al., 2008, MacArthur et al., 2009, Lucchetta et al., 2006)
Secondary FlyBase IDs
References ( 306 )
Generate a list of	All references relating to this gene ( 306 )
List References by type	Research paper  ( 191 ) Supplementary material  ( 5 ) Review  ( 49 ) Personal communication to FlyBase  ( 6 ) Abstract  ( 40 ) FlyBase analysis  ( 1 ) Stock list  ( 1 ) Curated genome annotation  ( 2 ) Protein sequence record  ( 1 ) DNA/RNA sequence record  ( 1 ) Computer file  ( 2 ) Automatic genome annotation  ( 1 ) Conference report  ( 2 ) Book  ( 1 ) Poem  ( 1 ) Interview  ( 1 )
Recent research papers ( 9 )
	Chatterjee et al., 2011, Development 138(6): 1099--1109 The female-specific Doublesex isoform regulates pleiotropic transcription factors to pattern genital development in Drosophila. [FBrf0213054] Fowlkes et al., 2011, PLoS Genet. 7(10): e1002346 A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. [FBrf0216666] Friedrich and Caravas, 2011, J. Exp. Zool. B Mol. Dev. Evol. 316(6): 387--392 New insights from hemichordate genomes: prebilaterian origin and parallel modifications in the paired domain of the Pax gene eyegone. [FBrf0214613] Pruteanu-Malinici et al., 2011, PLoS Comput. Biol. 7(7): e1002098 Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models. [FBrf0214618] Qian et al., 2011, Genomics 97(5): 294--303 The full-length transcripts and promoter analysis of intergenic microRNAs in Drosophila melanogaster. [FBrf0213652] Zhang and Arnosti, 2011, Mol. Cell. Biol. 31(2): 375--384 Conserved catalytic and C-terminal regulatory domains of the C-terminal binding protein corepressor fine-tune the transcriptional response in development. [FBrf0212606] Cunha et al., 2010, PLoS Genet. 6: e1001014 Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity. [FBrf0211225] Kazemian et al., 2010, PLoS Biol. 8(8): Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. [FBrf0211688] modENCODE Consortium et al., 2010, Science 330(6012): 1787--1797 Identification of functional elements and regulatory circuits by Drosophila modENCODE. [FBrf0212741] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...