FB2025_01 , released February 20, 2025
Gene: Dmel\DNAlig3
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General Information
Symbol
Dmel\DNAlig3
Species
D. melanogaster
Name
DNA ligase 3
Annotation Symbol
CG17227
Feature Type
protein_coding_gene
FlyBase ID
FBgn0286075
Gene Model Status
Current
Stock Availability
5 publicly available
Enzyme Name (EC)
DNA ligase (ATP) (6.5.1.1)
Gene Summary
DNA ligase 3 (DNAlig3) encodes an ATP-dependent DNA ligase that is involved in the repair of nuclear and mitochondrial single- and double-strand DNA breaks. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
All Summaries
Also Known As

lig3, DNA ligase III

Key Links
Genomic Location
Cytogenetic map
87B9-87B9
Sequence location
Recombination map
3-52
RefSeq locus
NT_033777 REGION:12399011..12401839
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
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables ATP binding
inferred from electronic annotation with InterPro:IPR000977, InterPro:IPR012310
(InterPro Project Members, 2004-)
enables DNA binding
inferred from electronic annotation with InterPro:IPR012308, InterPro:IPR036599
(InterPro Project Members, 2004-)
enables DNA ligase (ATP) activity
inferred from biological aspect of ancestor with PANTHER:PTN000048696
(GO Reference Genome Project, 2011-)
(InterPro Project Members, 2004-)
Biological Process (5 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
involved_in DNA biosynthetic process
inferred from electronic annotation with InterPro:IPR000977
(InterPro Project Members, 2004-)
involved_in DNA recombination
(InterPro Project Members, 2004-)
involved_in DNA repair
(InterPro Project Members, 2004-)
involved_in double-strand break repair
inferred from biological aspect of ancestor with PANTHER:PTN000825510
(GO Reference Genome Project, 2011-)
involved_in lagging strand elongation
inferred from biological aspect of ancestor with PANTHER:PTN000048696
(GO Reference Genome Project, 2011-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in mitochondrion
inferred from sequence or structural similarity with UniProtKB:P49916-1
(Gene Ontology Curators, 2002-)
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN002903640
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
DNA ligase (ATP) activity
ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate (6.5.1.1)
Summaries
Gene Snapshot
DNA ligase 3 (DNAlig3) encodes an ATP-dependent DNA ligase that is involved in the repair of nuclear and mitochondrial single- and double-strand DNA breaks. [Date last reviewed: 2019-03-07]
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.)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\DNAlig3 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
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VG84)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.53

Gene model reviewed during 5.45

Low-frequency RNA-Seq exon junction(s) not annotated.

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
DNAlig3-RA
FBtr0082600
NM_141930
2604
806
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
UniProt
RefSeq ID
GenBank
DNAlig3-PA
FBpp0082071
90.8
806
9.78
Q9VG84
NP_650187
AAF54801
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 properties of two DNA ligases purified from

embryos were compared. The enzymes differ in size, thermostability,

affinity for ATP, Km, and optimal reaction conditions (salt optima,

requirement for DTT, and reaction to PVA). They are similar in requirement

for ATP as cofactor and Mg2+ as divalent cation, inhibition by

N-ethylmaleimide, optimal ligation temp, and substrate specificity. The

major AMP-adduct has a molecular weight of 70kD.

(Takahashi and Senshu, 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\DNAlig3 using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.97

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data

DNAlig3 protein is concentrated in the nucleus.

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\DNAlig3 in JBrowse
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 3 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of DNAlig3
Transgenic constructs containing regulatory region of DNAlig3
Aberrations (Deficiencies and Duplications) ( 3 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
fertile
Other Phenotypes
Allele
abnormal flight, with Scer\GAL4Mef2.PR
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (3)
Hsap\LIG3
13 of 14
Yes
Yes
Hsap\LIG1
3 of 14
No
No
Hsap\LIG4
3 of 14
No
No
1  
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (3)
Rnor\Lig3
12 of 14
Yes
Yes
Rnor\Lig1
3 of 14
No
No
Rnor\Lig4
3 of 14
No
No
Mus musculus (laboratory mouse) (3)
Mmus\Lig3
13 of 14
Yes
Yes
Mmus\Lig4
3 of 14
No
No
Mmus\Lig1
2 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\lig3
7 of 13
Yes
Yes
Xtro\lig1
2 of 13
No
No
Xtro\lig4
2 of 13
No
No
Xtro\p4htm
1 of 13
No
No
Danio rerio (Zebrafish) (3)
Drer\lig3
13 of 14
Yes
Yes
Drer\lig1
3 of 14
No
No
Drer\lig4
3 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\K07C5.3
6 of 14
Yes
Yes
Cele\lig-4
3 of 14
No
No
Cele\Y73B6BL.14
3 of 14
No
Yes
Cele\lig-1
2 of 14
No
No
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP000623
3 of 12
Yes
No
Agam\AgaP_AGAP009222
3 of 12
Yes
No
Arabidopsis thaliana (thale-cress) (5)
Atha\LIG6
4 of 13
Yes
Yes
Atha\AT1G49250
3 of 13
No
No
Atha\ATLIG4
3 of 13
No
No
Atha\LIG1
3 of 13
No
No
Atha\AT5G17360
1 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\CDC9
2 of 13
Yes
No
Scer\DNL4
2 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\adl1
3 of 12
Yes
Yes
Spom\cdc17
2 of 12
No
No
Spom\lig4
2 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:DNAlig3. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
DNAlig1
5 of 13
DNAlig4
4 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 1 )
    Human Ortholog
    Disease
    Evidence
    References
    LIG3; DNA ligase 3
    model of  mitochondrial DNA depletion syndrome 20
    IEA
    (FlyBase, 2019-)
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 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?
    LIG3; DNA ligase 3
    13 of 14
    600940
    LIG1; DNA ligase 1
    3 of 14
    126391
      LIG4; DNA ligase 4
      3 of 14
      601837
       
      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
      Other Interaction Browsers
      Summary of Genetic Interactions
      esyN Network Diagram
      Other Interaction Browsers
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      External Data
      Linkouts
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      FlyBase
      External Links
      External Data
      Linkouts
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Class of Gene
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3R
      Recombination map
      3-52
      Cytogenetic map
      87B9-87B9
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      87B9-87B9
      Limits computationally determined from genome sequence between P{PZ}svp07842 and P{lacW}Vha55j2E9
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      3-52

      (FlyBase, 2016)

      3-49.5

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (5)
      Genomic Clones (15)
       

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

      cDNA Clones (16)
       

      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 JBrowse 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
        Antibody Information
        Laboratory Generated Antibodies
         
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments

            Mutagen studies with methylmethane sulfonate and camptothecin have demonstrated an extreme sensitivity in homozygous lig3 mutants. lig3 males have increased sensitivity relative to females.

            (Traynis and McVey, 2007)

            Purification and characterisation of DNA-ligII from pupae. DNA-ligII is distinct from DNA-ligI both in developmental appearance and biochemical properties.

            (Takahashi and Tomizawa, 1990)

            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)
            Relationship to Other Genes
            Source for database merge of

            Source for merge of: lig3 DNA-ligII

            (FlyBase, 1992-)
            Additional comments

            'DNA-ligII' (FBgn0013775) was an unannotated (non-CG) gene, created based on an enzymatic activity described by Takahashi and Senshu, 1987 (FBrf0046241) and Takahashi and Tomizawa, 1990 (FBrf0051704). The described characteristics of 'DNA-ligII' included: i) a relatively low activity throughout all developmental stages; ii) nuclear concentration; iii) thought to be similar to mammalian DNA ligase II. Of the two possible annotated candidates (DNA ligases 3 and 4), DNA ligase 3 is the best match - it's expressed at a low level throughout development, it's predicted to be nuclear, and it's the ortholog of mammalian LIG3 (aka LIG2). On this basis, 'DNA-ligII' was merged into the 'DNAlig3' report.

            (FlyBase, 1992-)
            Nomenclature History
            Source for database identify of

            Source for identity of: lig3 CG17227

            (Traynis, 2007.2.26)

            Source for identity of: DNAlig3 lig3

            (FlyBase, 2017-)
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (11)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
            UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
            Other crossreferences
            AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
            DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
            EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
            FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            MARRVEL_MODEL - MARRVEL (model organism gene)
            Linkouts
            FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            References (56)