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Gene Dmel\DNA-ligI

General Information
Symbol	Dmel\DNA-ligI	Species	D. melanogaster
Name	DNA ligase I	Annotation symbol	CG5602
Feature type	protein_coding_gene	FlyBase ID	FBgn0262619
Gene Model Status	Current	Stock availability	6 publicly available
Genomic Location
Chromosome (arm)	2R	Recombination map
Cytogenetic map	60A8-60A8	Sequence location	2R:19,778,061..19,780,700 [+]
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 DNA ligase I is referred to in FlyBase by the symbol Dmel\DNA-ligI (CG5602, FBgn0262619). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: DNA ligase (ATP) activity. An electronic pipeline based on InterPro domains suggests that it is involved in the biological process: DNA ligation involved in DNA repair; DNA recombination; DNA replication. 8 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide. Protein features are: DNA ligase, ATP-dependent; DNA ligase, ATP-dependent, C-terminal; DNA ligase, ATP-dependent, N-terminal; DNA ligase, ATP-dependent, central; DNA ligase, ATP-dependent, conserved site; Nucleic acid-binding, OB-fold; Nucleic acid-binding, OB-fold-like. Gene sequence location is 2R:19778061..19780700.
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.
FB2011_10
FB2012_01	Sequence features HFA04518
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 60A8-60A8   Limits computationally determined from genome sequence between P{lacW}kenk11035&P{EP}CG17658EP730 and P{EP}TalEP489&P{EP}CG3065EP316
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\DNA-ligI for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
	DGC clone appears problematic (LD41868): aberrant intron.
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) DNA-ligI-RA FBtr0072132  NM_137999   2360   747
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 DNA-ligI-PA   FBpp0072041   84.7   747   6.58     NP_611843   AAF47090
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments	The substrate specificity and mechanism of action of DNA-ligI protein are described. The joining reactions is shown to be reversible. (Rabin and Chase, 1987)
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • DNA ligase, ATP-dependent (IPR000977) DNA ligase, ATP-dependent, C-terminal (IPR012309) DNA ligase, ATP-dependent, central (IPR012310) Nucleic acid-binding, OB-fold (IPR012340) Nucleic acid-binding, OB-fold-like (IPR016027) DNA ligase, ATP-dependent, conserved site (IPR016059) DNA ligase, ATP-dependent, N-terminal (IPR012308)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA694934   AA695005   AA802092   AA978530   AE013599 AAF47090   AI516112   AI542725   AW943582   AY051939 AAK93363   BI370173   BI641495   BP554802   BT016103 AAV36988   CZ483382   GH748848   GH755026   GH756623   GH757023   GH757695   GH758411   GH759429   GH775527   GH780273   GH784961   GH789455   GH791043   GH792211   GH795779   GH798347   GH802066   GH810692   GH814658   GH818009   GH822349   GH823492   GH825095   GH827912   GH829698   GH832179   GH845169   GH847256   GH848073   GH854476   GH862408   GH864536   GH865334   GH867512   GH868542   GH869404   GH871527   GH872339   GH872745   GH873932   GH874465   GH878861   GH885151   GH892050   GH892807   GH894942   GH895342   GH896405   GH899324   GH906713   GH908483   GH910687   GH910920   GH911289   GH913383   GH914468   GH915874   GH919435   GH923608   GH929890   GH932535   GH935132   GH938993   GH939257   GH940212   GH940658
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9W1H4
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
Notes
Polypeptide Expression
enzyme assay or biochemical detection Stage Tissue/Position (including subcellular localization) Reference embryonic stage | early -- embryonic stage | mid     (Takahashi and Senshu, 1987)
Additional Descriptive Data
	Activity was high in 0-4hr embryos, lower in 8hr embryos and undetectable in 16hr embryos. (Takahashi and Senshu, 1987)
Marker for
Subcellular Localization
CV Term	cytoplasm (Takahashi and Senshu, 1987)
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. [an error occurred while processing this directive] 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_13
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Phenotype manifest in Allele
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of DNA-ligI Class Mutagen Stocks Known lesion DNA-ligIf00902 piggyBac transposase 2 --
Alleles Carried on Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Allele of DNA-ligI Class Mutagen Stocks Known lesion DNA-ligIGD4563 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes DNA-ligIHMS01036 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes DNA-ligIKK102537 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes DNA-ligItT1 in vitro construct - genomic fragment 0 Yes DNA-ligItT2 in vitro construct - genomic fragment 0 Yes DNA-ligItT3 in vitro construct - genomic fragment 0 Yes DNA-ligItT5 in vitro construct 0 Yes
Aneuploid Aberrations
Disrupted in	Df(2R)Exel6080 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{TRiP.HMS01036} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{WH}DNA-ligIf00902 NA
Gene Ontology: Function, Process & Cellular Component ( 8 unique terms )
Terms Based on Experimental Evidence ( 3 terms )
Molecular Function
CV term Evidence References
DNA ligase (ATP) activity inferred from direct assay (Rabin et al., 1986, Takahashi and Senshu, 1987)
Biological Process ( 0 terms)
Cellular Component
CV term Evidence References
cytoplasm inferred from direct assay (Takahashi and Senshu, 1987) NOT nuclear replication fork inferred from direct assay (Easwaran et al., 2007)
Terms Based on Predictions or Assertions ( 6 terms )
Molecular Function
CV term Evidence References
ATP binding inferred from electronic annotation with InterPro:IPR000977, InterPro:IPR012310 (FlyBase Curators et al., 2004-) DNA binding inferred from electronic annotation with InterPro:IPR012308 (FlyBase Curators et al., 2004-) DNA ligase (ATP) activity inferred from sequence or structural similarity with UniProtKB:P18858 AND inferred from sequence or structural similarity with UniProt:P51892 (FlyBase, 1992-)
Biological Process
CV term Evidence References
DNA ligation involved in DNA repair inferred from electronic annotation with InterPro:IPR016059 (FlyBase Curators et al., 2004-) DNA recombination inferred from electronic annotation with InterPro:IPR000977, InterPro:IPR012308, InterPro:IPR012309, InterPro:IPR012310 (FlyBase Curators et al., 2004-) DNA replication inferred from electronic annotation with InterPro:IPR000977 (FlyBase Curators et al., 2004-)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	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 DNA-ligI allele Gene References
External Data
Linkouts	DroID - A comprehensive database of gene and protein interactions. • FBgn0262619
Orthologs
Genome-wide drosophilid orthologs	Dana\GF12871 Dere\GG22898 Dgri\GH20192 Dmoj\GI20719 Dper\GL11174 Dpse\GA18999 Dsec\GM16058 Dsim\GD11806 Dvir\GJ20456 Dwil\GK15713 Dyak\GE14336
Curated drosophilid orthologs	Dpse\GA18999
Linkouts
Stocks & Reagents
Stocks Listed in FlyBase ( 6 )
Bloomington	18387 w1118; PBac{WH}DNA-ligIf00902/CyO 34564 y1 sc* v1; P{TRiP.HMS01036}attP2/TM3, Sb1
Harvard	- PBac{WH}DNA-ligIf00902
VDRC	v106463 P{KK102537}VIE-260B v51315 w1118; P{GD4563}v51315 v51316 w1118; P{GD4563}v51316/TM3
Genomic Clones ( 1 )
	BACR05F24 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 75 )
	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	LD20955 LD41868
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GM01816 GM01929 GM03841 LD30776 RE56591 SD09173 SD24846
Other clones	FGM231G10 RP003002277 RP003010469 RP003055853 RP003063045 RP003091988 RP003117551 RP003148901 RP003154020 RP003167757 RP003169903 RP003171605 RP003172786 RP003181415 RP003181704 RP003197055 RP003204132 RP003207515 RP003209916 RP003222177 RP003226409 RP003243152 RP003248129 RP003251375 RP003251624 RP003257920 RP003260914 RP003264402 RP003274578 RP003277946 RP003280269 RP003289168 RP003291668 RP003293128 RP003298589 RP003300265 RP003320405 RP003322647 RP003328960 RP003330575 RP003343803 RP003350612 RP003390881 RP003401969 RP003457328 RP003458731 RP003488940 RP003489872 RP003497069 RP003510435 RP003536905 RP003562075 RP003590173 RP003593763 RP003595340 RP003597861 RP003608015 RP003636006 RP003641898 RP003646493 RP003652086 RP003657711 RP003659937 RP003663285 RP003664362 RP003677823
RNAi & Array Information
Linkouts	GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 37791
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of	Source for merge of: DNA-ligI CG5602 (Easwaran et al., 2007)
Additional comments
Other Comments
	Identified as a potential component of the hh signalling pathway in a genome-wide RNAi screen. dsRNA made from templates generated with primers directed affects the extent of expression of a hh signaling reporter construct in Clone 8 cells. (Nybakken et al., 2005) The substrate specificity of DNA-ligI and its mechanism of action is described. The entire reaction sequence of DNA-ligI is demonstrated to be reversible. (Rabin and Chase, 1987) 2 distinct DNA ligases are present in embryos, DNA-ligI and DNA-ligII. They have similarities to mammalian DNA ligases I and II. This suggests there are two different DNA ligases in lower eukaryotes that may have different roles in DNA metabolism. (Takahashi and Senshu, 1987) DNA-ligI protein has been purified, the enzyme physically characterised in 6-12 hour embryos and enzyme activity during development studied. (Rabin et al., 1986)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_137999 RefSeq (Proteins) • NP_611843 DDBJ / EMBL / GenBank • AAF47090 AAK93363 AAV36988 AI516112 AW943582 AY051939 BT016103 CZ483382 Entrez Gene - A searchable database of RefSeq genes. • 37791 UniProtKB/TrEMBL • Q9W1H4
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • DNA ligase, ATP-dependent (IPR000977) DNA ligase, ATP-dependent, C-terminal (IPR012309) DNA ligase, ATP-dependent, central (IPR012310) Nucleic acid-binding, OB-fold (IPR012340) Nucleic acid-binding, OB-fold-like (IPR016027) DNA ligase, ATP-dependent, conserved site (IPR016059) DNA ligase, ATP-dependent, N-terminal (IPR012308)
Linkouts
	DroID - A comprehensive database of gene and protein interactions. • FBgn0262619 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 37791
Synonyms & Secondary IDs ( 4 )
Reported As
Symbol Synonym	CG5602 (Easwaran et al., 2007, Lin et al., 2006, Nybakken et al., 2005, Keleman et al., 2009.8.5, Lim et al., 2009, Ni et al., 2010.12.1) DmDNA Lig I (Easwaran et al., 2007) DNA-ligI
Name Synonym	DNA ligase I
Secondary FlyBase IDs
	FBgn0004596 FBgn0013774 FBgn0034922
References ( 24 )
Generate a list of	All references relating to this gene ( 24 )
List References by type	Research paper  ( 10 ) Supplementary material  ( 2 ) Personal communication to FlyBase  ( 6 ) FlyBase analysis  ( 1 ) Computer file  ( 3 ) Curated genome annotation  ( 1 ) Automatic genome annotation  ( 1 )
Recent research papers (0)
	All research papers listed in FlyBase were published before 2010 Show research papers ...