A Database of Drosophila Genes & Genomes

FB2012_01, released January 20th, 2012
 

Gene Dmel\CG9666

General Information
SymbolDmel\CG9666SpeciesD. melanogaster
NameAnnotation symbolCG9666
Feature typeprotein_coding_geneFlyBase IDFBgn0036856
Gene Model StatusCurrent Stock availability 4 publicly available
Genomic Location
Chromosome (arm)3LRecombination map
Cytogenetic map76A3-76A3Sequence location3L:19,256,869..19,259,938 [+]

Genomic Maps

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modENCODE GBrowse
detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
This gene is referred to in FlyBase by the symbol Dmel\CG9666 (FBgn0036856). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: site-specific DNA-methyltransferase (adenine-specific) activity. An electronic pipeline based on InterPro domains suggests that it is involved in the biological process: methylation. 8 alleles are reported. No phenotypic data is available. It has 2 annotated transcripts and 2 annotated polypeptides. Protein features are: DNA methylase, N-6 adenine-specific, conserved site; Methyltransferase small. 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 00-12 hour embryonic stages. This gene is annotated by FlyBase as a dicistronic gene, meaning that some or all of its transcripts encode two or more polypeptide-coding open reading frames (ORFs) , with each ORF assigned to a different gene. The distribution of RNA-Seq coverage data amongst the different encoded genes cannot be determined. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: larval central nervous system, adult ovary, adult testis. Comments on Affy2 ProbeSet: ProbeSet 1633418_at aligns to a genomic region shared by exons of 2 FlyBase-annotated genes; hence it is impossible to interpret the expression pattern and levels of CG9666 expression signal. See the GBrowse view of CG9666 to determine the overlapping gene(s). Gene sequence location is 3L:19256869..19259938.

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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
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
76A3-76A3  
Limits computationally determined from genome sequence between P{EP}MESR6EP3142 and P{lacW}l(3)L3809L3809  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
hide Gene Model & Products
Please see the GBrowse view of Dmel\CG9666 for information on other features
To submit a correction to a gene model please use the Contact FlyBase form
detailed view FBtr0074990 FBtr0074989 FBtr0074991 FBtr0299975 FBtr0299974 FBtr0310276 FBtr0075018 FBtr0075017 FBpp0074758 FBpp0074757 FBpp0301959 FBpp0074785 FBpp0289252 FBpp0074759 FBpp0289251 FBpp0074784 FBti0043140 FBti0039331 FBti0102200 FBti0100060 FBti0027166 FBti0058316 FBti0125802_2 FBti0125802_1
Comments on Gene Model
gene_with_dicistronic_mRNA ; SO:0000722
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
CG9666-RA
FBtr0074991
 NM_140841
  1632
  213
CG9666-RB
FBtr0299974
 NM_001144501
  1030
  213
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
CG9666-PA  
FBpp0074759  
24.0  
213  
6.40  
  NP_649098
  AAF49178
CG9666-PB  
FBpp0289251  
24.0  
213  
6.40  
  NP_001137973
  ACL83328
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
DNA methylase, N-6 adenine-specific, conserved site (IPR002052)
Methyltransferase small (IPR007848)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA816361
 
AA941348
 
AA948935
 
AE014296
AAF49178
 
AE014296
ACL83328
 
AI517151
 
AW942731
 
AY060320
 
AY118530
AAM49899
 
BF500534
 
BI161661
 
BI161662
 
BI169072
 
BI170192
 
BI173235
 
BI213702
 
BI230914
 
BI231521
 
BI241045
 
BI241051
 
BI241058
 
BI241067
 
BI241075
 
BI242556
 
BI362635
 
BI363908
 
BI364359
 
BI365465
 
BI365945
 
BI367422
 
BI375407
 
BI481913
 
BI580593
 
CA805294
 
CA805370
 
CK660450
 
CL527900
 
CO182425
 
CO319012
 
CO319559
 
CO326668
 
EC052212
 
EC053692
 
EC066961
 
EC194903
 
EC204490
 
EC246098
 
EC259057
 
EL883478
 
GH775342
 
GH778684
 
GH783399
 
GH785909
 
GH790719
 
GH793536
 
GH803699
 
GH804421
 
GH810975
 
GH812876
 
GH814621
 
GH815635
 
GH842566
 
GH854678
 
GH865818
 
GH867858
 
GH868131
 
GH871528
 
GH887441
 
GH888612
 
GH900741
 
GH901129
 
GH902125
 
GH906387
 
GH909127
 
GH912468
 
GH913111
 
GH916257
 
GH918453
 
GH920611
 
GH933932
 
GH940478
 
 
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
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
hidePolypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
hide High-Throughput Expression Data
or
Untitled Document detailed view CG9666-RA CG42374-RA CG9666-RB Max-RC Max-RA CG9629-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 CG9666
hide Alleles & Phenotypes
hide Summary of Allele Phenotypes
Lethality
Allele
lethal
viable
Sterility
Allele
fertile
Other Phenotypes
Allele
wild-type
Phenotype manifest in
Allele
hide Classical Alleles ( 6 )
For All Classical Alleles Show

Allele of CG9666ClassMutagenStocksKnown lesion
CG9666EY027751 Yes
CG9666EY064311 Yes
CG9666PL004641 Yes
CG9666CB045030 Yes
CG9666DfMax1
0 Yes
CG9666DfMax2
0 Yes
hide Alleles Carried on Transgenic Constructs ( 2 )
For All Alleles Carried on Transgenic Constructs Show

Allele of CG9666ClassMutagenStocksKnown lesion
CG9666GD42191 Yes
CG9666t2.7880 Yes
hide Aneuploid Aberrations
hide Transgenic Constructs & Insertions
Transgenic Constructs
Type of construct
Name
Expression data
UAS construct
P{GD4219}
NA
characterization construct
P{Max+t2.788}
NA
Insertions
Type of insertions
Name
Expression data
insertion of mobile activating element
P{EPgy2}CG9666EY02775
NA
P{EPgy2}CG9666EY06431
NA
insertion of enhancer trap binary system
PBac{GAL4D,EYFP}CG9666PL00464
No
miscellaneous insertions
P{PTT-GB}CG9666CB04503
NA
hide Gene Ontology: Function, Process & Cellular Component ( 3 unique terms )
hide Terms Based on Experimental Evidence ( 0 terms )
hide Terms Based on Predictions or Assertions ( 3 terms )
Molecular Function
CV term
Evidence
References
nucleic acid binding
inferred from electronic annotation with InterPro:IPR002052
(FlyBase Curators et al., 2004-)
site-specific DNA-methyltransferase (adenine-specific) activity
inferred from sequence or structural similarity with InterPro:IPR002296
(FlyBase, 1992-)
Biological Process
CV term
Evidence
References
methylation
inferred from electronic annotation with InterPro:IPR002052
(FlyBase Curators et al., 2004-)
Cellular Component ( 0 terms)
hide Sequence Ontology: Class of Gene
gene_with_dicistronic_mRNA
(FlyBase Genome Annotators, 2008)
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
CG9666 allele
Gene
References
hide External Data
Linkouts
BioGRID - A database of protein and genetic interactions
•
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
 
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 ( 4 )
Bloomington
15596
y1 w67c23; P{EPgy2}CG9666EY02775 CG42374EY02775
16723
y1 w67c23; P{EPgy2}CG9666EY06431 CG42374EY06431
19514
w*; PBac{GAL4D,EYFP}PL00464 PBac{GAL4D,EYFP}CG9666PL00464 CG42374PL00464 P{FRT(whs)}2A P{neoFRT}82B
VDRC
v45658
w1118; P{GD4219}v45658/TM3
hide Genomic Clones ( 2 )

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
hide cDNA Clones ( 74 )

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
hide Other Information
hide Discoverer
hide Etymology
hide Identification
hide Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG9666 and CG42374.
(FlyBase Genome Annotators, 2008)
hide Other Comments
hide External Crossreferences & Linkouts
Sequence Crossreferences
RefSeq (Transcripts)
•
RefSeq (Proteins)
•
DDBJ / EMBL / GenBank
•
Entrez Gene - A searchable database of RefSeq genes.
•
UniProtKB/TrEMBL
•
Other Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
DNA methylase, N-6 adenine-specific, conserved site (IPR002052)
Methyltransferase small (IPR007848)
Linkouts
BioGRID - A database of protein and genetic interactions
•
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.
•
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 ( 2 )
Reported As
Symbol Synonym
CG9666
(Steiger et al., 2008, FlyBase Genome Annotators, 2008, Buszczak et al., 2007, Hayden and Bosco, 2008, Steiger et al., 2008, Spresser et al., 2008)
Dromel_CG9666_FBtr0074991_mORF
(Hayden and Bosco, 2008)
Name Synonym
Secondary FlyBase IDs
hide References ( 18 )
Research paper
Hayden and Bosco, 2008, BMC Genomics 9: 61
Comparative genomic analysis of novel conserved peptide upstream open reading frames in Drosophila melanogaster and other dipteran species. [FBrf0204849]
Spresser et al., 2008, J. Genet. 87(2): 109--117
Characterization of gene expression regulated by human OTK18 using Drosophila melanogaster as a model system for innate immunity. [FBrf0205982]
Steiger et al., 2008, Nat. Genet. 40(9): 1084--1091
Max-independent functions of Myc in Drosophila melanogaster. [FBrf0206679]
Buszczak et al., 2007, Genetics 175(3): 1505--1531
The Carnegie protein trap library: A versatile tool for Drosophila developmental studies. [FBrf0200345]
Bjorklund et al., 2006, Nature 439(7079): 1009--1013
Identification of pathways regulating cell size and cell-cycle progression by RNAi. [FBrf0191233]
Supplementary material
The modENCODE Consortium, 2010, Science 330(6012):
DataS14: Gene co-expression clusters. [FBrf0213979]
Hayden and Bosco, 2008, BMC Genomics:
File 1: Conserved peptide uORF and associated mORF amino acid sequences in Drosophila melanogaster. [FBrf0205942]
Steiger et al., 2008, Nature Genetics 40(9):
Supplementary information. [FBrf0208289]
Giot et al., 2003, Science 302(5651):
Tables S1 to S7. [FBrf0166452]
Personal communication to FlyBase
Dickson et al., 2007.7.18, RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center
RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0200327]
FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms.
Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215]
Haecker et al., 2004, Haecker insertions.
Haecker insertions. [FBrf0184338]
Robertson, 2001.5.6, FlyBase error report on Sun May 06 00:40:30 2001.
FlyBase error report on Sun May 06 00:40:30 2001. [FBrf0136023]
FlyBase analysis
FlyBase Genome Annotators, 2008, Changes affecting gene model number or type in release 5.10 of the annotated D.melanogaster genome.
Changes affecting gene model number or type in release 5.10 of the annotated D.melanogaster genome. [FBrf0204955]
FlyBase, 1996-, FlyBase inference based on genome sequence analysis.
FlyBase inference based on genome sequence analysis. [FBrf0104946]
FlyBase, 1992-, FlyBase curation
FlyBase curation. [FBrf0105495]
Computer file
Gene Disruption Project members, 2001-, [title not yet available]
[title not yet available] [FBrf0132177]
BDGP Project Members, 2000-, Berkeley Drosophila Genome Project.
Berkeley Drosophila Genome Project. [FBrf0125078]