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Gene Dmel\slx1

General Information
Symbol	Dmel\slx1	Species	D. melanogaster
Name	nuclease slx1	Annotation symbol	CG18271
Feature type	protein_coding_gene	FlyBase ID	FBgn0037263
Gene Model Status	Current	Stock availability	3 publicly available
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	82C5-82C5	Sequence location	3R:467,685..470,358 [+]
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 nuclease slx1 is referred to in FlyBase by the symbol Dmel\slx1 (CG18271, FBgn0037263). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: protein binding. There is experimental evidence that it is involved in the biological process: mitotic G2 DNA damage checkpoint. 6 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide. Protein features are: GIY-YIG domain; GIY-YIG nuclease superfamily. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of very low expression. Peak expression observed within 00-12 hour embryonic stages, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Little or no expression detected in any larval or adult organs/tissues. Comments on Affy2 ProbeSet: ProbeSet 1632047_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of CG18271. Gene sequence location is 3R:467685..470358.
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.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03	Controlled Vocabulary Terms DNA repair 5'-flap endonuclease activity
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 82C5-82C5   Limits computationally determined from genome sequence between P{PZ}l(3)0273302733 and P{EP}EP974
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\slx1 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 5.47 Shares 5' UTR with upstream gene.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) slx1-RB FBtr0301296  NM_141227   1139   297
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 slx1-PB   FBpp0290511   34.1   297   6.50     NP_649484   AAF52110
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • GIY-YIG nuclease superfamily (IPR000305) Structure-specific endonuclease subunit Slx1 (IPR027520) GIY-YIG domain (IPR027299)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014297 AAF52110   BG636757   BI352024   BT001465   BT029079   CO289000   CO345183   EC056717   EC070035   EC079777   EC219055   EC255211   EC256393   EL879726   EL879854   EL879985
UniProtKB/Swiss-Prot	Q9VN41
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
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_13 mE1_20_mRNA_expression_cluster_06
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0037263 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG18271-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Other Phenotypes Allele radiation sensitive, with Scer\GAL4ap-md544 slx1TRiP.HMS00313 Phenotype manifest in Allele
Classical Alleles ( 3 )
For All Classical Alleles Show
Allele of slx1 Class Mutagen Stocks Known lesion slx1e01051 1 -- slx1F93I 0 Yes slx1HKK1 FLPase 0 Yes
Alleles Carried on Transgenic Constructs ( 3 )
For All Alleles Carried on Transgenic Constructs Show
Allele of slx1 Class Mutagen Stocks Known lesion slx1HMS00505 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes slx1TRiP.HMS00313 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes slx1GD9550 in vitro construct - RNAi in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Not disrupted in	Df(3R)rpk-Karyβ3 (Tsubouchi et al., 2012)
Partially disrupted in	Df(3R)HKK1 (Andersen et al., 2011) Dp(3;3)HKK2 (Andersen et al., 2011)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{TRiP.HMS00313} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{RB}slx1e01051 NA
Gene Ontology: Function, Process & Cellular Component ( 6 unique terms )
Terms Based on Experimental Evidence ( 2 terms )
Molecular Function
CV term Evidence References
protein binding inferred from physical interaction with mus312 (Andersen et al., 2009)
Biological Process
CV term Evidence References
mitotic G2 DNA damage checkpoint inferred from mutant phenotype (Kondo and Perrimon, 2011)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 4 terms )
Molecular Function
CV term Evidence References
5'-flap endonuclease activity inferred from electronic annotation with InterPro:IPR027520 (FlyBase Curators et al., 2004-) endodeoxyribonuclease activity inferred from sequence or structural similarity with Saccharomyces SLX1 (Curators, 2008--)
Biological Process
CV term Evidence References
DNA repair inferred from electronic annotation with InterPro:IPR027520 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
Slx1-Slx4 complex inferred from sequence or structural similarity with Saccharomyces SLX1 (Curators, 2008--)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions slx1 allele Gene References
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 65797 DroID - A comprehensive database of gene and protein interactions. • FBgn0037263 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 40578
Orthologs
OrthoDB Orthologs (40) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search EOG6TMRN9 Dipteran inclusive ortholog search EOG68WC9Z Insect inclusive ortholog search EOG6X3FX8 Arthropod inclusive ortholog search EOG61JWV2 Metazoa inclusive ortholog search EOG6JB0T2
Orthologs in Drosophila Species (EOG6TMRN9)
Organism Common Name Gene AAA Syntenic Ortholog Multiple Dmel Genes in this Orthologous Group Drosophila melanogaster fruit fly  Dmel\slx1     Drosophila simulans   Dsim\GD17776 Y   Drosophila sechellia   Dsec\GM10768 Y   Drosophila erecta   Dere\GG12527 Y   Drosophila yakuba   Dyak\GE14944     Drosophila yakuba   Dyak\GE25427 Y   Drosophila ananassae   Dana\GF16665 Y   Drosophila pseudoobscura pseudoobscura   Dpse\GA27368 Y   Drosophila persimilis   Dper\GL22073 Y   Drosophila willistoni   Dwil\GK19194 Y   Drosophila virilis   Dvir\GJ23950 Y   Drosophila mojavensis   Dmoj\GI23768 Y   Drosophila grimshawi   Dgri\GH19497 Y
Orthologs in non-Drosophila Dipterans (EOG68WC9Z)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Aedes aegypti Yellow fever mosquito  Aaeg\AAEL004139   Aedes aegypti Yellow fever mosquito  Aaeg\AAEL004145   Anopheles gambiae Malaria mosquito  Agam\AGAP002259   Culex quinquefasciatus Southern house mosquito  Cqui\CPIJ013689
Orthologs in non-Dipteran Insects (EOG6X3FX8)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Apis mellifera Western honey bee  Amel\GB42934   Nasonia vitripennis Parasitic wasp  Nvit\Nasvi2EG013500   Acromyrmex echinatior Panamanian leafcutter ant  Aech\AECH26203   Atta cephalotes Leafcutter ant  Acep\ACEP20349   Camponotus floridanus Florida carpenter ant  Cflo\CFLO15028   Harpegnathos saltator Jerdons jumping ant  Hsal\HSAL22763   Linepithema humile Argentine ant  Lhum\LH19272   Pogonomyrmex barbatus Red harvester ant  Pbar\PB12190   Solenopsis invicta Red fire ant  Sinv\SINV12241   Acyrthosiphon pisum Pea aphid  Apim\ACYPI010123   Pediculus humanus Human body louse  Phum\PHUM609030   Tribolium castaneum Red flour beetle  Tcas\GLEAN_15403
Orthologs in non-Insect Arthropods (EOG61JWV2)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Daphnia pulex Water flea  Dpux\JGI_V11_306753   Ixodes scapularis Deer tick  Isca\ISCW019252
Orthologs in non-Arthropod Metazoa (EOG6JB0T2)
Organism Common Name Gene Multiple Dmel Genes in this Orthologous Group Caenorhabditis elegans Nematode  Cele\giyd-1   Strongylocentrotus purpuratus Purple sea urchin  Spur\SPU_011930gn   Danio rerio Zebrafish  Drer\ENSDARG00000077494   Xenopus tropicalis Western clawed frog  Xtro\ENSXETG00000029925   Gallus gallus Domestic chicken  Ggal\LOC424727   Mus musculus House mouse  Mmus\Slx1b   Rattus norvegicus Norway rat  Rnor\Slx1b   Homo sapiens Human  Hsap\ENSG00000181625   Homo sapiens Human  Hsap\ENSG00000132207
Human Orthologs (2)
Gene OMIM HGNC Hsap\ENSG00000181625     Hsap\ENSG00000132207
AAA Orthologs (11) based on analysis using Dmel annotation version 4.3
Organism Gene Drosophila simulans Dsim\GD17776 Drosophila sechellia Dsec\GM10768 Drosophila erecta Dere\GG12527 Drosophila yakuba Dyak\GE25427 Drosophila ananassae Dana\GF16665 Drosophila pseudoobscura pseudoobscura Dpse\GA27368 Drosophila persimilis Dper\GL22073 Drosophila willistoni Dwil\GK19194 Drosophila virilis Dvir\GJ23950 Drosophila mojavensis Dmoj\GI23768 Drosophila grimshawi Dgri\GH19497
Stocks & Reagents
Stocks Listed in FlyBase ( 3 )
Bloomington	32501 y1 sc* v1; P{TRiP.HMS00505}attP2 34949 y1 sc* v1; P{TRiP.HMS00313}attP2
Harvard	- PBac{RB}slx1e01051
Genomic Clones ( 1 )
	BACR07E06 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 15 )
	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	GM28912 IP09950
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GM17275 SD14538
Other clones	214351.68 214473.72 CK01.2D.D10 CK01.82B.C7 CK01.88D.G2 CK01.112C.C3 EK069857 EP21547 IP09650 IP09750 IP09850
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0037263 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 40578
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: slx1 CG18271 (Kondo and Perrimon, 2011)
Source for database merge of
Additional comments	FlyBase Curator comment: Authors refer to 'Drosophila SLX1'. At time of curation (Sept 2009), this symbol did not exist in FlyBase. A BLAST search using the S. cerevisiae Slx1 sequence as a query gave D. melanogaster CG18271 as the only high scoring hit. (Andersen et al., 2009)
Other Comments
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_141227 RefSeq (Proteins) • NP_649484 DDBJ / EMBL / GenBank • AAF52110 Entrez Gene - A searchable database of RefSeq genes. • 40578 UniProtKB/Swiss-Prot • Q9VN41
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • GIY-YIG nuclease superfamily (IPR000305) Structure-specific endonuclease subunit Slx1 (IPR027520) GIY-YIG domain (IPR027299)
Linkouts
	BioGRID - A database of protein and genetic interactions • 65797 DroID - A comprehensive database of gene and protein interactions. • FBgn0037263 DRSC - Results from RNAi screens. • FBgn0037263 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0037263 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG18271-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0037263 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 40578 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 40578 modMine - Data generated by the modENCODE project. • FBgn0037263
Synonyms & Secondary IDs ( 5 )
Reported As
Symbol Synonym	CG18271 (Tsubouchi et al., 2012, Kondo and Perrimon, 2011, Ni et al., 2010.12.1, Ni et al., 2011.7.19, Andersen et al., 2011) SLX1 (Andersen et al., 2009) slx1 (Kondo and Perrimon, 2011, Andersen et al., 2011)
Name Synonym	nuclease SLX1 (Kondo and Perrimon, 2011) nuclease slx1
Secondary FlyBase IDs
References ( 14 )
Research paper	Tsubouchi et al., 2012, Curr. Biol. 22(22): 2124--2134 Dendritic Filopodia, Ripped Pocket, NOMPC, and NMDARs Contribute to the Sense of Touch in Drosophila Larvae. [FBrf0219946] Andersen et al., 2011, PLoS Genet. 7(10): e1002315 Three Structure-Selective Endonucleases Are Essential in the Absence of BLM Helicase in Drosophila. [FBrf0216460] Kondo and Perrimon, 2011, Sci. Signal. 4(154): rs1 A Genome-Wide RNAi Screen Identifies Core Components of the G2-M DNA Damage Checkpoint. [FBrf0212700] Andersen et al., 2009, Mol. Cell 35(1): 128--135 Drosophila MUS312 and the vertebrate ortholog BTBD12 interact with DNA structure-specific endonucleases in DNA repair and recombination. [FBrf0208485]
Supplementary material	Graveley et al., 2011, Nature 471(7339): Supplementary Table 33. Fuzzy Cluster Members. [FBrf0213980] The modENCODE Consortium, 2010, Science 330(6012): DataS14: Gene co-expression clusters. [FBrf0213979] Dietzl et al., 2007, Nature 448(7150): Supplementary Table 1. [FBrf0202579] Giot et al., 2003, Science 302(5651): Tables S1 to S7. [FBrf0166452]
Personal communication to FlyBase	Ni et al., 2011.7.19, TRiP germline vector pVALIUM21. TRiP germline vector pVALIUM21. [FBrf0214641] Ni et al., 2010.12.1, A genome-scale shRNA resource for transgenic RNAi in Drosophila. A genome-scale shRNA resource for transgenic RNAi in Drosophila. [FBrf0212437] 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]
FlyBase analysis	FlyBase Curators, 2010-, Gene Ontology (GO) annotation review. Gene Ontology (GO) annotation review. [FBrf0216433] Curators, 2008--, Assigning Gene Ontology (GO) terms by sequence similarity in FlyBase. Assigning Gene Ontology (GO) terms by sequence similarity in FlyBase. [FBrf0202953] FlyBase Curators, 2008, Insertion identifiers and alleles based on genomic location of insertions with respect to gene annotations. Insertion identifiers and alleles based on genomic location of insertions with respect to gene annotations. [FBrf0202955]