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Gene Dmel\Snp

General Information
Symbol	Dmel\Snp	Species	D. melanogaster
Name	Snipper	Annotation symbol	CG44248
Feature type	protein_coding_gene	FlyBase ID	FBgn0265192
Gene Model Status	Current	Stock availability	13 publicly available
Also Known As	CG6393, CG42257
Genomic Location
Chromosome (arm)	2R	Recombination map
Cytogenetic map	58B1-58B2	Sequence location	2R:17,948,455..17,957,262 [+]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents Beta	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene Snipper is referred to in FlyBase by the symbol Dmel\Snp (CG44248, FBgn0265192). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: double-stranded DNA specific 3'-5' exodeoxyribonuclease activity; single-stranded DNA specific 3'-5' exodeoxyribonuclease activity; 3'-5'-exoribonuclease activity. The biological processes in which it is involved are not known. 13 alleles are reported. The phenotypes of these alleles are annotated with: trichogen cell; mesothoracic tergum. It has 4 annotated transcripts and 4 annotated polypeptides. Protein features are: Exonuclease; Exonuclease, RNase T/DNA polymerase III; Ribonuclease H-like domain. Gene sequence location is 2R:17948455..17957262.
User Contributed Data
	Beta version, feedback welcome
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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FB2013_03
FB2013_02
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 58B1-58B2   Limits computationally determined from genome sequence between P{PZ}l(2)0783707837 and P{EP}CG6393EP2457
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Snp for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	Gene model reviewed during 5.49 Shares 5' UTR with upstream gene. Low-frequency RNA-Seq exon junction(s) not annotated.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Snp-RD FBtr0339099     1899   281 Snp-RE FBtr0339100     1578   223 Snp-RF FBtr0339101     1419   223 Snp-RG FBtr0339102     1667   223
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Snp-PD   FBpp0308244   32.1   281   8.26       Snp-PE   FBpp0308245   25.7   223   8.26       Snp-PF   FBpp0308246   25.7   223   8.26       Snp-PG   FBpp0308247   25.7   223   8.26
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Exonuclease (IPR006055) Ribonuclease H-like domain (IPR012337) Exonuclease, RNase T/DNA polymerase III (IPR013520)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA263520   AA391778   AA441173   AA541162   AI296949   AQ073603   AW942394   AX094060   AY061211 AAL28759   BF487049   BF492221   BF499304   BG638248   BI167184   BI237334   BI241156   BI364988   BI365071   BI374339   BI578972   BI613145   BI615229   BT016135   BT024321   BT031103   CL526015   CO262860   CO269876   CO276029   CO286563   CO308757   CO310759   CO310968   CO311063   CO312653   CO316427   CO318404   CZ466478   CZ469495   EC071235   EC077691   EC080690   EC082790   EC082916   EC086489   EC087603   EC087616   EC088616   EC201978   EC208086   EC219490   EC225804   EC226201   EC226844   EC238799   EC248037   EC249549   EL881261   EV576518   EV593103   EV596629
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q95RQ4
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 3   organism   (Fisher et al., 2012) Comment:maternally deposited embryonic stage 4 -- 6   organism | ubiquitous   • cytoplasm | basal (Fisher et al., 2012) Comment:apically cleared embryonic stage 7 -- 8   organism | faint & ubiquitous   (Fisher et al., 2012) embryonic stage 9 -- 10   organism | faint & ubiquitous   (Fisher et al., 2012) embryonic stage 11 -- 12   anterior midgut primordium   (Fisher et al., 2012) fat body/gonad primordium   (Fisher et al., 2012) posterior midgut primordium   (Fisher et al., 2012) embryonic stage 13 -- 16   embryonic anal pad   (Fisher et al., 2012) embryonic main segment of Malpighian tubule   (Fisher et al., 2012) embryonic/larval fat body   (Fisher et al., 2012) embryonic/larval midgut   (Fisher et al., 2012)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
[an error occurred while processing this directive] FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
modENCODE Anatomy RNA-Seq
[an error occurred while processing this directive]
modENCODE Development RNA-Seq
[an error occurred while processing this directive] modENCODE Temporal Expression Data (Graveley et al., 2011)
modENCODE Cell Lines RNA-Seq
[an error occurred while processing this directive]
modENCODE Treatments RNA-Seq
[an error occurred while processing this directive]
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, Graveley et al., 2011) mE2_34_mRNA_expression_cluster_27 mE1_20_mRNA_expression_cluster_02
External Data & Images
Linkouts	BDGP expression data • LD16074 CG6393
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele partially lethal - majority die | pupal stage, with Scer\GAL4pnr-MD237 SnpGD11912 viable Snpc00465 SnpEP2457 SnpEY08427 SnpEY16388 viable (with Df(2R)Exel7170) Snpc00465 SnpEP2457 Sterility Allele fertile Snpc00465 SnpEP2457 SnpEY08427 SnpEY16388 fertile (with Df(2R)Exel7170) Snpc00465 SnpEP2457 Other Phenotypes Allele visible, with Scer\GAL4pnr-MD237 SnpGD11912 Phenotype manifest in Allele mesothoracic tergum, with Scer\GAL4pnr-MD237 SnpGD11912 trichogen cell, with Scer\GAL4pnr-MD237 SnpGD11912
Classical Alleles ( 9 )
For All Classical Alleles Show
Allele of Snp Class Mutagen Stocks Known lesion Snpc00465 piggyBac transposase 2 Yes SnpEP2457 P-element activity 2 Yes Snpc04761 piggyBac transposase 1 -- Snpc06824 1 -- SnpEY08427 P-element activity 1 -- SnpEY16388 P-element activity 1 Yes SnpSH1834 1 -- SnpEY01513 P-element activity 0 -- SnpMI07339 0 --
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Snp Class Mutagen Stocks Known lesion SnpGD11912 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes SnpHMS00321 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes SnpKK108801 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes SnpNIG.6393R in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{NIG.6393R} NA P{TRiP.HMS00321} NA
Insertions
	Type of insertions Name Expression data insertion of mobile activating element P{EP}SnpEP2457 NA P{EPgy2}SnpEY01513 NA P{EPgy2}SnpEY08427 NA P{EPgy2}SnpEY16388 NA miscellaneous insertions Mi{MIC}SnpMI07339 NA PBac{PB}Snpc00465 NA PBac{PB}Snpc04761 NA PBac{PB}Snpc06824 NA insertion of enhancer trap P{lacW}SnpSH1834 No
Gene Ontology: Function, Process & Cellular Component ( 6 unique terms )
Terms Based on Experimental Evidence ( 4 terms )
Molecular Function
CV term Evidence References
3'-5'-exoribonuclease activity inferred from direct assay (Kupsco et al., 2006) double-stranded DNA specific 3'-5' exodeoxyribonuclease activity inferred from direct assay (Kupsco et al., 2006) single-stranded DNA specific 3'-5' exodeoxyribonuclease activity inferred from direct assay (Kupsco et al., 2006)
Biological Process
CV term Evidence References
NOT histone mRNA catabolic process inferred from mutant phenotype (Kupsco et al., 2006)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 2 terms )
Molecular Function
CV term Evidence References
nucleic acid binding inferred from electronic annotation with InterPro:IPR012337 (FlyBase Curators et al., 2004-)
Biological Process ( 0 terms)
Cellular Component
CV term Evidence References
intracellular inferred from electronic annotation with InterPro:IPR006055 (FlyBase Curators et al., 2004-)
Sequence Ontology: Class of Gene
	nuclear_gene (FlyBase Genome Annotators, 2012) protein_coding_gene (FlyBase Genome Annotators, 2012)
Interactions & Pathways
Summary of Physical Interactions
protein-protein
Interacting group Assay References
Snp - Arp2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Arpc1 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Arpc2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - CG10802 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - CG2862 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - CG3689 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - CG6321 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - CG8036 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - CG8239 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - CG9947 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Crc anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Elongin-B anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Eno anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Mfe2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Pdi anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Prosβ7 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - Trx-2 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - cathD anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - cpb anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - fabp anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - mus209 anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23) Snp - regucalcin anti tag coimmunoprecipitation, peptide massfingerprinting (Mintseris et al., 2009.11.23)
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Snp allele Gene References
External Data
Linkouts
Orthologs
OrthoDB Orthologs (34) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups - Dmel gene model changed subsequent to version 5.45
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6NKCFK Dipteran inclusive ortholog search EOG6G4H04 Insect inclusive ortholog search EOG6CVF3M Arthropod inclusive ortholog search EOG602V7T Metazoa inclusive ortholog search EOG6D2KHQ
Orthologs in Drosophila Species (EOG6NKCFK)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\CG44249     Drosophila melanogaster fruit fly  Dmel\Snp     Drosophila erecta   Dere\GG22156 Y Y Drosophila yakuba   Dyak\GE12236 Y Y Drosophila ananassae   Dana\GF13283 Y Y Drosophila pseudoobscura pseudoobscura   Dpse\GA25008 Y Y Drosophila persimilis   Dper\GL16971 Y Y Drosophila willistoni   Dwil\GK15943 Y Y Drosophila mojavensis   Dmoj\GI18815 Y Y Drosophila grimshawi   Dgri\GH20545 Y Y
Orthologs in non-Drosophila Dipterans (EOG6G4H04)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL005083 Y Anopheles gambiae Malaria mosquito  Agam\AGAP005296 Y Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ003638 Y
Orthologs in non-Dipteran Insects (EOG6CVF3M)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB42263 Y Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG009561 Y Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH22208 Y Atta cephalotes Leafcutter ant  Acep\ACEP17613 Y Camponotus floridanus Florida carpenter ant  Cflo\CFLO20049 Y Linepithema humile Argentine ant  Lhum\LH15229 Y Pogonomyrmex barbatus Red harvester ant  Pbar\PB18163 Y Solenopsis invicta Red fire ant  Sinv\SINV13872 Y Acyrthosiphon pisum Pea aphid  Apim\ACYPI009870 Y Bombyx mori Silkmoth  Bmor\BGIBMGA011921 Y Pediculus humanus Human body louse  Phum\PHUM293630 Y Tribolium castaneum Red flour beetle  Tcas\TC010372 Y
Orthologs in non-Insect Arthropods (EOG602V7T)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\Ehd3 Y Ixodes scapularis Deer tick  Isca\ISCW012575 Y
Orthologs in non-Arthropod Metazoa (EOG6D2KHQ)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_002130gn Y Danio rerio Zebrafish  Drer\rnpc3 Y Xenopus tropicalis Western clawed frog  Xtro\rnpc3 Y Gallus gallus Domestic chicken  Ggal\RNPC3 Y Mus musculus House mouse  Mmus\Rnpc3 Y Rattus norvegicus Norway rat  Rnor\Rnpc3 Y Homo sapiens Human  Hsap\RNPC3 Y
Human Orthologs (1)
Gene OMIM HGNC Hsap\RNPC3
AAA Orthologs (19) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD11641 Drosophila sechellia Dsec\GM15878 Drosophila erecta Dere\GG22156 Drosophila erecta Dere\GG22157 Drosophila yakuba Dyak\GE12236 Drosophila yakuba Dyak\GE12237 Drosophila ananassae Dana\GF13283 Drosophila ananassae Dana\GF13284 Drosophila pseudoobscura pseudoobscura Dpse\GA25008 Drosophila pseudoobscura pseudoobscura Dpse\GA25009 Drosophila persimilis Dper\GL16971 Drosophila persimilis Dper\GL16972 Drosophila willistoni Dwil\GK15943 Drosophila willistoni Dwil\GK15944 Drosophila virilis Dvir\GJ21843 Drosophila mojavensis Dmoj\GI18815 Drosophila mojavensis Dmoj\GI18816 Drosophila grimshawi Dgri\GH20545 Drosophila grimshawi Dgri\GH20546
Stocks & Reagents
Stocks Listed in FlyBase ( 13 )
Bloomington	10182 w1118; PBac{PB}Snpc00465 17060 w1118; P{EP}SnpEP2457/CyO 17462 y1 w67c23; P{EPgy2}SnpEY08427 21207 y1 w67c23; P{EPgy2}SnpEY16388 33434 y1 sc* v1; P{TRiP.HMS00321}attP2 29507 w*; P{FRT(whs)}G13 P{lacW}SnpSH1834, l(2)SH1834SH1834/CyO
Harvard	- PBac{PB}Snpc00465 - PBac{PB}Snpc04761 - PBac{PB}Snpc06824
VDRC	v105744 P{KK108801}VIE-260B v40376 w1118; P{GD11912}v40376 v40377 w1118; P{GD11912}v40377
	More stocks available...
Genomic Clones ( 1 )
	BACR30O14 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 53 )
	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	GH06496 IP10959 LD16074
Other clones	DPiM_LD16074 IP11159
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT13835 AT21721 AT29117 LD06675 LD11541 LP11078 RE07514 RE33548 RE38173 RE50203 RE50291 RE61902 RE72929 RH42236 RH44810
Other clones	70642 97187 100012 100377 100554 109134 122227 125812 153631 155625 160973 166776 CK01.51A.H11 CK01.102D.E12 CK01.125C.D11 CK01.131B.G6 CK01.145B.H8 Dmel_dig_007714_0641_2292 Dmel_neb_014823_0897_2817 Dmel_neb_015356_0667_2282 EK063230 EK086550 EK096216 EK119464 EK222441 EK223056 EK223245 EK229602 EK259254 EK264936 EK271941 IP11059 LD20991
RNAi & Array Information
Linkouts
Antibody Information
Other Information
Discoverer
Etymology
	The gene is named "Snipper" based on its potent exonucleolytic activity in vitro. (Kupsco et al., 2006)
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: Snp CG42257 (Kupsco et al., 2006)
Source for database merge of	Source for merge of: CG30327 CG6393 (FlyBase Genome Annotators, 2008)
Additional comments	Annotation CG42257 split into CG44248 (which corresponds to Snp) and CG44249 in release 5.49 of the genome annotation. (FlyBase Genome Annotators, 2012) Split based in part on on data from FBrf0191914. (FlyBase Genome Annotators, 2012) Annotations CG30327 and CG6393 merged as CG42257 in release 5.8 of the genome annotation. (FlyBase Genome Annotators, 2008)
Other Comments
	Area matching Drosophila EST AA441173. (Davies, 2001.3.15)
External Crossreferences & Linkouts
Sequence Crossreferences
	DDBJ / EMBL / GenBank • AA441173 AAL28759 AQ073603 AW942394 AX094060 AY061211 CL526015 CZ466478 CZ469495 Entrez Gene - A searchable database of RefSeq genes. • 37511 UniProtKB/TrEMBL • Q95RQ4
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Exonuclease (IPR006055) Ribonuclease H-like domain (IPR012337) Exonuclease, RNase T/DNA polymerase III (IPR013520) BDGP expression data - Patterns of gene expression in Drosophila embryogenesis • CG6393 LD16074
Linkouts
Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym	CG6393 (Giot et al., 2003, Japanese National Institute of Genetics, 2012.5.21, Zaratiegui, 2007, Keleman et al., 2009.8.5, Kupsco et al., 2006) CG11478   CG30327   CG42257 (FlyBase Genome Annotators, 2008, Ni et al., 2010.12.1) CG44248 (FlyBase Genome Annotators, 2012, ) Snp (FlyBase Genome Annotators, 2012, Kupsco et al., 2006)
Name Synonym	Snipper (Kupsco et al., 2006, )
Secondary FlyBase IDs
	FBgn0034685 FBgn0259142 FBgn0265183
References ( 27 )
Generate a list of	All references relating to this gene ( 27 )
List References by type	Research paper  ( 2 ) Supplementary material  ( 5 ) Review  ( 1 ) Personal communication to FlyBase  ( 10 ) FlyBase analysis  ( 5 ) Stock list  ( 1 ) Patent  ( 1 ) DNA/RNA sequence record  ( 1 ) Website  ( 1 )
Recent research papers (0)
	All research papers listed in FlyBase were published before 2011 Show research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2011 Show reviews ...