A Database of Drosophila Genes & Genomes

FB2012_01, released January 20th, 2012
 

Gene Dmel\pit

General Information
SymbolDmel\pitSpeciesD. melanogaster
NamepitchouneAnnotation symbolCG6375
Feature typeprotein_coding_geneFlyBase IDFBgn0025140
Gene Model StatusCurrent Stock availability 6 publicly available
Genomic Location
Chromosome (arm)3RRecombination map
Cytogenetic map94A1-94A1Sequence location3R:17,860,020..17,864,114 [+]

Genomic Maps

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modENCODE GBrowse
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Automatically generated summary

See sections below for more information
The gene pitchoune is referred to in FlyBase by the symbol Dmel\pit (CG6375, FBgn0025140). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: ATP-dependent RNA helicase activity; RNA helicase activity. The biological processes in which it is involved are not known. 11 alleles are reported. The phenotype of these alleles is annotated with: wing disc. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: DEAD-like helicase; DNA/RNA helicase, DEAD/DEAH box type, N-terminal; Helicase, C-terminal; RNA helicase, DEAD-box type, Q motif. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-18 hour embryonic stages, during early larval stages, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult ovary. Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system, larval hindgut, adult fat body, larval salivary gland, larval trachea, adult spermathecae, adult male accessory gland, larval carcass. Comments on Affy2 ProbeSet: ProbeSet 1625758_s_at completely aligns to an exonic region common to each of the 2 FlyBase-annotated transcript isoforms of pit. Gene sequence location is 3R:17860020..17864114.

External Summaries

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Description
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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
Andersen et al., 2010, Mol. Cell. Biol. 30(19): 4744--4755
Sequence features
BKN26435
HFA17025
FB2011_10
All updates Click here to see a list of all updates to this record from FB2010_08 and on.
hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
94A1-94A1  
Limits computationally determined from genome sequence between P{PZ}tsl00617 and P{lacW}howj5B5&P{EP}EP738  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
93F-93F  
 
(Zaffran, 1997.1.9)
93F-93F  
(determined by in situ hybridisation)  
(Zaffran et al., 1998)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
hide Gene Model & Products
Please see the GBrowse view of Dmel\pit for information on other features
To submit a correction to a gene model please use the Contact FlyBase form
detailed view FBtr0084183 FBtr0084174 FBtr0084176 FBtr0084175 FBtr0309756 FBpp0083581 FBpp0083574 FBpp0083573 FBpp0083572 FBti0128406 FBti0110116 FBti0057879 FBti0042613 FBti0126205_2 FBti0126205_1 FBti0050838 FBti0057605 FBti0106705 FBti0126206 FBti0033659 FBti0066976
Comments on Gene Model
Translation start as per accession U84552
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
pit-RA
FBtr0084175
 NM_079722
  2198
  680
pit-RB
FBtr0084174
 NM_169991
  2324
  680
Additional Transcript Data & Comments
Reported size (kB)
2.4 (northern blot)
(Zaffran et al., 1998)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
pit-PA  
FBpp0083573  
76.9  
680  
8.19  
  NP_524446
  AAF55951
pit-PB  
FBpp0083572  
76.9  
680  
8.19  
  NP_732694
  AAN13900
Additional Polypeptide Data & Comments
Reported size (kDa)
772 (aa); 75 (kD predicted)
(Zaffran et al., 1998)
Comments
External Data
Linkouts
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Helicase, C-terminal (IPR001650)
DNA/RNA helicase, DEAD/DEAH box type, N-terminal (IPR011545)
DEAD-like helicase (IPR014001)
RNA helicase, DEAD-box type, Q motif (IPR014014)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA264486
 
AA391394
 
AA391611
 
AA392010
 
AA950178
 
AE014297
AAF55951
 
AE014297
AAN13900
 
AI514629
 
AI514630
 
AI516618
 
AW943823
 
AY071402
AAL49024
 
AY119620
AAM50274
 
BF494209
 
BF504870
 
BI353160
 
BI363871
 
BI365432
 
BI576713
 
BI580904
 
BI581645
 
BI582168
 
BI585270
 
BI604546
 
BI606277
 
BI611873
 
BI611887
 
BI611912
 
BI620816
 
BI623953
 
BI631048
 
BI631228
 
BI631252
 
CK135063
 
CO262263
 
CO264198
 
CO275601
 
CO278070
 
CO282894
 
CO291072
 
CO291260
 
CO329051
 
CO339039
 
EC059100
 
EC061083
 
EC084114
 
EC084448
 
EC198457
 
EC219268
 
EC226790
 
EC231943
 
EC245494
 
EC258860
 
GH752130
 
GH756942
 
GH760810
 
GH770537
 
GH772361
 
GH775399
 
GH778509
 
GH778943
 
GH781275
 
GH791409
 
GH794337
 
GH795174
 
GH806464
 
GH808626
 
GH814517
 
GH815917
 
GH817748
 
GH824417
 
GH838245
 
GH840134
 
GH853969
 
GH855271
 
GH856463
 
GH866494
 
GH869290
 
GH880677
 
GH884531
 
GH889947
 
GH893909
 
GH898763
 
GH899827
 
GH906463
 
GH921670
 
GH925672
 
GH932660
 
GH932924
 
GH935608
 
GH936274
 
U84552
AAC27683
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
hide 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
hide External Data
Linkouts
Crossreferences
hide Expression Data
hideTranscript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage | early  
organism | ubiquitous  
(Zaffran et al., 1998)
gastrula stage  
mesoderm  
(Zaffran et al., 1998)
embryonic stage 11  
embryonic/larval salivary gland | precursor  
(Zaffran et al., 1998)
anal plate  
(Zaffran et al., 1998)
embryonic stage 11 -- 17  
anterior midgut primordium  
(Zaffran et al., 1998)
posterior midgut primordium  
(Zaffran et al., 1998)
embryonic stage 16  
epithelial sheath of embryonic/larval midgut  
(Zaffran et al., 1998)
Malpighian tubule  
(Zaffran et al., 1998)
embryonic/larval midgut  
(Zaffran et al., 1998)
gonadal sheath  
(Zaffran et al., 1998)
epithelial sheath of embryonic/larval hindgut  
(Zaffran et al., 1998)
larval stage  
imaginal disc | ubiquitous  
(Zaffran et al., 1998)
adult stage & oogenesis  
germarium  
(Zaffran et al., 1998)
oogenesis stage S4 -- S14 & adult stage | female  
egg chamber  
(Zaffran et al., 1998)
Additional Descriptive Data
pit transcripts are uniformly distributed in pre-blastoderm embryos. At gastrulation, pit is expressed in the invaginating mesoderm. At stage 11, expression is observed in the mesoderm in the anterior and posterior midgut precursors and in the salivary gland precursors. Strong expression is also seen in the anal plate. In later stages, expression is limited to the midgut, the Malpighian tubules and the mesodermal sheath of gonads. At stage 16 pit transcripts are observed in the entire epithelial sheet of the intestine. In ovaries, pit transcripts are observed in the germarium and then in egg chambers from stage 4 on. Ubiquitous expression is observed in imaginal discs.
(Zaffran et al., 1998)
Marker for
Subcellular Localization
CV Term
Notes
hidePolypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
nucleolus
(Zaffran et al., 1998)
Notes
hide High-Throughput Expression Data
or
Untitled Document detailed view CG6015-RA pit-RB BG4-RA pit-RA scaRNA:mgU5-38-RA
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
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modENCODE Temporal Expression Data (Graveley et al., 2011)
FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
hide Expression Clusters
A cluster of genes with similar mRNA expression dynamics across development.
(The modENCODE Consortium, 2010)
hide External Data & Images
Linkouts
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
•
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
•
FlyExpress - Embryonic expression images (BDGP data)
•
Show all FlyExpress processed images for pit
hide Alleles & Phenotypes
hide Summary of Allele Phenotypes
Lethality
Allele
lethal | pupal stage, with Scer\GAL4pnr-MD237
lethal | recessive
viable
Sterility
Allele
fertile
Phenotype manifest in
Allele
adult midgut precursor cell | larval stage
embryonic/larval midgut | embryonic stage
embryonic/larval salivary gland | embryonic stage
imaginal precursor | larval stage
wing disc, with Scer\GAL4en-e16E
wing disc | posterior compartment, with Scer\GAL4en-e16E
hide Classical Alleles ( 6 )
For All Classical Alleles Show

Allele of pitClassMutagenStocksKnown lesion
pitf069542 --
pitEY10870
1 --
pitEY14017
1 --
pit10loss of function allele0 Yes
pit40 Yes
pit50 Yes
hide Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show

Allele of pitClassMutagenStocksKnown lesion
pitGD119051 Yes
pitKK1064351 Yes
piths.T:Hsap\MYC0 Yes
pitmod.PZ0 Yes
pitScer\UAS.cZa0 Yes
hide Aneuploid Aberrations
Disrupted in
(Zaffran et al., 1998)
(Ryder, 2004.4.26)
hide Transgenic Constructs & Insertions
Transgenic Constructs
Type of construct
Name
Expression data
UAS construct
P{GD11905}
NA
P{KK106435}
NA
P{UAS-pit.Z}
NA
characterization construct
P{mod-pit.Z}
NA
Insertions
Type of insertions
Name
Expression data
insertion of mobile activating element
P{EPgy2}BG4EY10870
NA
P{EPgy2}BG4EY14017
NA
miscellaneous insertions
P{?lacW}pit10
NA
PBac{WH}BG4f02804
NA
PBac{WH}BG4f06954
NA
hide Gene Ontology: Function, Process & Cellular Component ( 6 unique terms )
hide Terms Based on Experimental Evidence ( 0 terms )
hide Terms Based on Predictions or Assertions ( 6 terms )
Molecular Function
CV term
Evidence
References
ATP binding
inferred from electronic annotation with InterPro:IPR001650, InterPro:IPR011545
(FlyBase Curators et al., 2004-)
ATP-dependent RNA helicase activity
inferred from sequence or structural similarity with Saccharomyces HAS1
(FlyBase, 1992-)
non-traceable author statement
(Swiss-Prot Project Members, 2000.10.1)
nucleic acid binding
inferred from electronic annotation with InterPro:IPR001650, InterPro:IPR011545
(FlyBase Curators et al., 2004-)
RNA helicase activity
inferred from sequence or structural similarity with Saccharomyces HAS1
(Lasko, 2000)
Biological Process ( 0 terms)
Cellular Component
CV term
Evidence
References
nucleolus
non-traceable author statement
(Swiss-Prot Project Members, 2000.10.1)
nucleus
non-traceable author statement
(Swiss-Prot Project Members, 2000.10.1)
hide Sequence Ontology: Class of Gene
nuclear_gene
 
protein_coding_gene
 
hide Interactions & Pathways
hide Summary of Physical Interactions
Protein-protein
Interacting group
Assay
References
hide Summary of Genetic Interactions
Interacts with
Please look at the allele data for full details of the genetic interactions
pit allele
Gene
References
hide External Data
Linkouts
BioGRID - A database of protein and genetic interactions
•
DPiM - DPiM, Drosophila Protein interaction Map
•
DroID - A comprehensive database of gene and protein interactions.
•
InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets.
•
hide Orthologs
Genome-wide drosophilid orthologs
Curated drosophilid orthologs
 
(Begun, 2000.4.5)
Linkouts
InParanoid A subset of ortholog calls from InParanoid.
•
OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs.
•
hide Stocks & Reagents
hide Stocks Listed in FlyBase ( 6 )
Bloomington
19026
w1118; PBac{WH}BG4f06954 pitf06954
20638
y1 w67c23; P{EPgy2}BG4EY10870 pitEY10870
20904
y1 w67c23; P{EPgy2}BG4EY14017 pitEY14017
Harvard
-
PBac{WH}BG4f06954
VDRC
v106078
P{KK106435}VIE-260B
v27600
w1118; P{GD11905}v27600
hide Genomic Clones ( 2 )

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
hide cDNA Clones ( 86 )

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
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones
hide RNAi & Array Information
Linkouts
DRSC - Results from RNAi screens.
•
GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents
•
hide Antibody Information
polyclonal
(Zaffran et al., 1998)
hide Other Information
hide Discoverer
hide Etymology
The gene is named "pitchoune" (meaning "small" in the Provencal language) after the phenotype of mutant larvae, which do not grow beyond the first instar stage but can survive for as long as 7-10 days.
(Zaffran et al., 1998)
hide Identification
hide Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
scaRNA:mgU5-38 is encoded in an intron of pit.
(Graveley et al., 2011)
hide Other Comments
dsRNA made from templates generated with primers directed against this gene in combination with dsRNA against gig results in suppression of the final average cell size, with it being closer to the control average cell size, rather than the average cell size resulting from knockdown of the candidate gene alone.
(Guertin et al., 2006)
dsRNA made from templates generated with primers directed against pit that is transfected into S2 treated with Listeria monocytogenes reveals pit to be involved in Listeria monocytogenes intracellular growth and vacuolar escape.
(Cheng et al., 2005)
pit is required for cell growth and proliferation.
(Zaffran et al., 1998)
hide External Crossreferences & Linkouts
Sequence Crossreferences
RefSeq (Transcripts)
•
RefSeq (Proteins)
•
DDBJ / EMBL / GenBank
•
Entrez Gene - A searchable database of RefSeq genes.
•
UniProtKB/Swiss-Prot
•
Other Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Helicase, C-terminal (IPR001650)
DNA/RNA helicase, DEAD/DEAH box type, N-terminal (IPR011545)
DEAD-like helicase (IPR014001)
RNA helicase, DEAD-box type, Q motif (IPR014014)
Linkouts
BioGRID - A database of protein and genetic interactions
•
DPiM - DPiM, Drosophila Protein interaction Map
•
DroID - A comprehensive database of gene and protein interactions.
•
DRSC - Results from RNAi screens.
•
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
•
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
•
FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
•
GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents
•
InParanoid A subset of ortholog calls from InParanoid.
•
Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
•
InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets.
•
modMine - Data generated by the modENCODE project.
•
OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs.
•
hide Synonyms & Secondary IDs ( 6 )
Reported As
Symbol Synonym
CG6375
(Guertin et al., 2006, Cakouros et al., 2008, Keleman et al., 2009.8.5)
DmRH15
(Boudet et al., 2001)
PIT
(Boudet et al., 2001)
pit
(Furrer et al., 2010, FlyBase Curators, 2008, Rhodes et al., 2010, Graveley et al., 2011)
Pit
(Andersen et al., 2010)
Name Synonym
pitchoune
 
Secondary FlyBase IDs
hide References ( 43 )
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hide Recent research papers ( 3 )
Andersen et al., 2010, Mol. Cell. Biol. 30(19): 4744--4755
Drosophila MCRS2 Associates with RNA Polymerase II Complexes To Regulate Transcription. [FBrf0211794]
Furrer et al., 2010, J. Biol. Chem. 285(51): 39623--39636
Drosophila Myc Interacts with Host Cell Factor (dHCF) to Activate Transcription and Control Growth. [FBrf0212501]
Rhodes et al., 2010, Dev. Biol. 344(2): 637--649
Positive regulation of c-Myc by cohesin is direct, and evolutionarily conserved. [FBrf0211404]
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