FB2020_04, released Aug 18, 2020

Gene: Dmel\DNAlig1

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General Information
Symbol
Dmel\DNAlig1
Species
D. melanogaster
Name
DNA ligase 1
Annotation Symbol
CG5602
Feature Type
protein_coding_gene
FlyBase ID
FBgn0262619
Gene Model Status
Current
Stock Availability
8 publicly available
Enzyme Name (EC)
DNA ligase (ATP) (6.5.1.1)
Gene Snapshot
Contributions welcome
Other Summaries
Also Known As

DNA-ligI, DNA ligase I

Key Links
Genomic Location
Cytogenetic map
60A8-60A8
Sequence location
2R:23,890,512..23,893,177 [+]
Recombination map

2-105

RefSeq locus
NT_033778 REGION:23890512..23893177
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (13 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
DNA ligase (ATP) activity
inferred from direct assay
(Takahashi and Senshu, 1987, Rabin et al., 1986)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
ATP binding
inferred from electronic annotation with InterPro:IPR000977, InterPro:IPR012310
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
DNA binding
inferred from electronic annotation with InterPro:IPR012308
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
DNA ligase (ATP) activity
inferred from biological aspect of ancestor with PANTHER:PTN000048696
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (6 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (6 terms)
CV Term
Evidence
References
DNA biosynthetic process
inferred from electronic annotation with InterPro:IPR000977
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
DNA ligation
inferred from biological aspect of ancestor with PANTHER:PTN000048696
(assigned by GO_Central )
(Gaudet et al., 2011)
DNA ligation involved in DNA repair
inferred from biological aspect of ancestor with PANTHER:PTN000048696
(assigned by GO_Central )
(Gaudet et al., 2011)
DNA recombination
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
lagging strand elongation
inferred from biological aspect of ancestor with PANTHER:PTN000048696
(assigned by GO_Central )
(Gaudet et al., 2011)
Okazaki fragment processing involved in mitotic DNA replication
inferred from biological aspect of ancestor with PANTHER:PTN000048794
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
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 (3 terms)
CV Term
Evidence
References
cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000048696
(assigned by GO_Central )
(Gaudet et al., 2011)
mitochondrion
inferred from biological aspect of ancestor with PANTHER:PTN000048763
(assigned by GO_Central )
(Gaudet et al., 2011)
nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000048763
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the ATP-dependent DNA ligase family. (Q9W1H4)
Protein Signatures (InterPro)
Catalytic Activity (EC)
Experimental Evidence
ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate (6.5.1.1)
Predictions / Assertions
ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate (6.5.1.1)
Summaries
Gene Group (FlyBase)
DNA LIGASES -
DNA ligases join adjacent 3'-hydroxyl and 5'-phosphoryl termini to form a phosphodiester bond in duplex DNA and thus have an indispensable role in DNA replication, recombination, and repair. (Adapted from PMID:23959747.)
Protein Function (UniProtKB)
DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.
(UniProt, Q9W1H4)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\DNAlig1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
DNAlig1-RA
FBtr0072132
NM_137999
2386
747
Additional Transcript Data and 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
DNAlig1-PA
FBpp0072041
84.7
747
6.58
NP_611843
AAF47090
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments

The substrate specificity and mechanism of action of DNAlig1 protein are described. The joining reactions is shown to be reversible.

(Rabin and Chase, 1987)
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\DNAlig1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
enzyme assay or biochemical detection
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 8
organism
(Takahashi and Senshu, 1987)
Additional Descriptive Data

DNAlig1 protein is found in the cytoplasmic fraction of embryonic extracts.

(Takahashi and Senshu, 1987)
Marker for
 
Subcellular Localization
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)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\DNAlig1 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 12 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of DNAlig1
Transgenic constructs containing regulatory region of DNAlig1
Deletions and Duplications ( 1 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
partially lethal, with Scer\GAL4tin.CΔ4
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\LIG1
15 of 15
Yes
Yes
Hsap\LIG3
2 of 15
No
No
Hsap\LIG4
1 of 15
No
No
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Lig1
14 of 15
Yes
Yes
Mmus\Lig3
2 of 15
No
No
Mmus\Lig4
2 of 15
No
No
Rattus norvegicus (Norway rat) (4)
Rnor\Lig1
12 of 13
Yes
Yes
Rnor\LOC100911727
8 of 13
No
Yes
Rnor\Lig4
2 of 13
No
No
Rnor\Lig3
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\lig1
9 of 12
Yes
Yes
Xtro\lig3
2 of 12
No
No
Xtro\lig4
2 of 12
No
No
Xtro\LOC101731611
1 of 12
No
Yes
Danio rerio (Zebrafish) (3)
Drer\lig1
13 of 15
Yes
Yes
Drer\lig3
2 of 15
No
No
Drer\lig4
2 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\lig-1
15 of 15
Yes
Yes
Cele\K07C5.3
2 of 15
No
No
Cele\lig-4
2 of 15
No
No
Cele\Y73B6BL.14
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (4)
Atha\LIG1
9 of 9
Yes
Yes
Atha\AT1G49250
8 of 9
No
Yes
Atha\ATLIG4
1 of 9
No
No
Atha\LIG6
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\CDC9
14 of 15
Yes
Yes
Scer\DNL4
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\cdc17
11 of 12
Yes
Yes
Spom\adl1
1 of 12
No
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919030B )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00002188
Drosophila simulans
Dsim\GD11806
Drosophila sechellia
Dsec\GM13668
Drosophila sechellia
Dsec\GM16058
Drosophila erecta
Dere\GG22898
Drosophila yakuba
Dyak\GE14336
Drosophila ananassae
Dana\GF12871
Drosophila pseudoobscura pseudoobscura
Dpse\GA18999
Drosophila persimilis
Dper\GL11174
Drosophila willistoni
Dwil\GK15713
Drosophila virilis
Dvir\GJ20456
Drosophila mojavensis
Dmoj\GI20719
Drosophila grimshawi
Dgri\GH20192
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504N7 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17019963
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_02293
Mayetiola destructor
Hessian fly
Mdes\Mdes008633
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL017566
Anopheles darlingi
American malaria mosquito
Adar\ADAC005036
Anopheles gambiae
Malaria mosquito
Agam\AGAP009222
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015601
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015499
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ003597
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015498
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ013855
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015528
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ009862
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ014787
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015371
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015051
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ008932
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W04H0 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA009181
Danaus plexippus
Monarch butterfly
Dple\DPOGS212214-PA
Danaus plexippus
Monarch butterfly
Dple\DPOGS203534-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL005760
Apis florea
Little honeybee
Aflo\2921393124
Apis mellifera
Western honey bee
Amel\GB55848
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP13939
Bombus terrestris
Buff-tailed bumblebee
Bter\15215746
Linepithema humile
Argentine ant
Lhum\LH18862
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG009638
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_09817
Tribolium castaneum
Red flour beetle
Tcas\TC003800
Pediculus humanus
Human body louse
Phum\PHUM175060
Rhodnius prolixus
Kissing bug
Rpro\RPRC003933
Cimex lectularius
Bed bug
Clec\CLEC001818
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI007879
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_08184
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X04DN )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR002567
Stegodyphus mimosarum
African social velvet spider
Smim\KFM71353.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur02g07210
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_304798
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G06OS )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Dnl1
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000005638
Gallus gallus
Domestic chicken
Ggal\ENSGALG00000013384
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (2)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
DNAlig3
4 of 10
DNAlig4
3 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    LIG1; DNA ligase 1
    15 of 15
    126391
        Functional Complementation Data
        Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
        Interactions
        Summary of Physical Interactions
        esyN Network Diagram
        Interactions Browser
        Summary of Genetic Interactions
        esyN Network Diagram
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map

        2-105

        Cytogenetic map
        60A8-60A8
        Sequence location
        2R:23,890,512..23,893,177 [+]
        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

        2-105

        (FlyBase, 2016)

        2-109.6

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (8)
        Genomic Clones (17)
         

        Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

        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
          Drosophila Genomics Resource Center cDNA clones

          For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

          cDNA Clones, End Sequenced (ESTs)
          BDGP DGC clones
          Other clones
          RNAi and Array Information
          Linkouts
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          Antibody Information
          Laboratory Generated Antibodies
           
          Commercially Available Antibodies
           
          Other Information
          Relationship to Other Genes
          Source for database identify of

          Source for identity of: DNAlig1 DNA-ligI

          (FlyBase, 2017-)
          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)
          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 35 )
          Sequence Crossreferences
          NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
          GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
          GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
          RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
          UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
          Other crossreferences
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          Linkouts
          DroID - A comprehensive database of gene and protein interactions.
          KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          Synonyms and Secondary IDs (8)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (45)