FlyBase Gene Report: Dmel\DNAlig1

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 Summary

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. (UniProt, Q9W1H4)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

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

JBrowse GBrowse

Help me choose

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

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

enables 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

enables ATP binding

inferred from electronic annotation with InterPro:IPR000977, InterPro:IPR012310

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables DNA binding

inferred from electronic annotation with InterPro:IPR012308

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables DNA ligase (ATP) activity

inferred from biological aspect of ancestor with PANTHER:PTN005231428

(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

involved_in DNA biosynthetic process

inferred from electronic annotation with InterPro:IPR000977

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

involved_in DNA ligation

inferred from biological aspect of ancestor with PANTHER:PTN005231428

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in DNA recombination

inferred from electronic annotation with InterPro:IPR000977, InterPro:IPR012308, InterPro:IPR012309, InterPro:IPR012310

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

involved_in DNA repair

inferred from electronic annotation with InterPro:IPR000977, InterPro:IPR012308, InterPro:IPR012309, InterPro:IPR012310, InterPro:IPR036599

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

involved_in lagging strand elongation

inferred from biological aspect of ancestor with PANTHER:PTN000048696

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in 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

located_in cytoplasm

inferred from direct assay

(Takahashi and Senshu, 1987)

NOT located_in nuclear replication fork

inferred from direct assay

(Easwaran et al., 2007)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN005231428

(assigned by GO_Central )

(Gaudet et al., 2011)

is_active_in mitochondrion

inferred from biological aspect of ancestor with PANTHER:PTN000048763

(assigned by GO_Central )

(Gaudet et al., 2011)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000048763

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

DNA LIGASES

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

Number of Unique Polypeptides

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

Structure New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9W1H4)

If you don't see the viewer to the right, 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.

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

Nucleotide / Polypeptide Records

UniProt

Q9W1H4

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.

DNA-ligI_1

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

located_in cytoplasm

inferred from direct assay

(Takahashi and Senshu, 1987)

NOT located_in 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

View exonic expression by developmental stage for Dmel\DNAlig1

View exonic expression by tissue for Dmel\DNAlig1

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

37791/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0262619

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0034922

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0262619

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG5602

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 ( 12 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of DNAlig1

Transgenic constructs containing regulatory region of DNAlig1

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2R)Exel6080

(Ryder, 2004.4.26)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

partially lethal, with Scer\GAL4^tin.CΔ4

DNAlig1^GD4563

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (3)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\LIG1

15 of 15

Yes

Hsap\LIG3

2 of 15

Hsap\LIG4

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (3)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Lig1

14 of 15

Yes

Mmus\Lig3

2 of 15

Mmus\Lig4

2 of 15

Rattus norvegicus (Norway rat) (4)

Rnor\Lig1

12 of 13

Yes

Rnor\LOC100911727

8 of 13

Yes

Rnor\Lig4

2 of 13

Rnor\Lig3

1 of 13

Xenopus tropicalis (Western clawed frog) (4)

Xtro\lig1

9 of 12

Yes

Xtro\lig3

2 of 12

Xtro\lig4

2 of 12

Xtro\LOC101731611

1 of 12

Yes

Danio rerio (Zebrafish) (3)

Drer\lig1

13 of 15

Yes

Drer\lig3

2 of 15

Drer\lig4

2 of 15

Caenorhabditis elegans (Nematode, roundworm) (4)

Cele\lig-1

15 of 15

Yes

Cele\K07C5.3

2 of 15

Cele\lig-4

2 of 15

Cele\Y73B6BL.14

1 of 15

Arabidopsis thaliana (thale-cress) (4)

Atha\LIG1

9 of 9

Yes

Atha\AT1G49250

8 of 9

Yes

Atha\ATLIG4

1 of 9

Atha\LIG6

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\CDC9

14 of 15

Yes

Scer\DNL4

1 of 15

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\cdc17

11 of 12

Yes

Spom\adl1

1 of 12

Yes

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (2)

Gene Symbol

Score

Source

Alignment

4 of 10

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

IMMUNODEFICIENCY 96; IMD96

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.

FBgn0262619

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0262619

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Genomic Location and Detailed Mapping Data

Chromosome (arm)

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}ken^k11035&P{EP}CG17658^EP730 and P{EP}Tal^EP489&P{EP}CG3065^EP316

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)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

52951

y¹ v¹; P{TRiP.HMJ21620}attP40

18387

w¹¹¹⁸; PBac{WH}DNAlig1^f00902/CyO

77099

y¹ sc^* v¹ sev²¹; P{TKO.GS00894}attP40

78197

y¹ sc^* v¹ sev²¹; P{TOE.GS01372}attP40

34564

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01036}attP2/TM3, Sb¹

Kyoto

201604

y¹ w^67c23; P{GSV7}DNAlig1^GS20555/SM1

VDRC

v106463

P{KK102537}VIE-260B

v51315

w¹¹¹⁸; P{GD4563}v51315

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.

FBgn0262619

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

37791

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 ( 43 )

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.

37791

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.

Q9W1H4

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9W1H4

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.

Q9W1H4

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0262619

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

37791/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0262619

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

DNA-ligI_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0034922

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0262619

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG5602

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0262619

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

37791

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC003800

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

Dmel_CG5602

MARRVEL_MODEL - MARRVEL (model organism gene)

37791

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262619

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 (9)

Reported As

Symbol Synonym

CG5602

(Kolkhof et al., 2017, Barclay et al., 2014, Japanese National Institute of Genetics, 2012.5.21, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Lim et al., 2009, Easwaran et al., 2007, Lin et al., 2006, Nybakken et al., 2005)

DNA-lig1

(Ferguson et al., 2021)

DNA-ligI

(Transgenic RNAi Project members, 2017-, Van Bortle et al., 2015, Barclay et al., 2014, Liang et al., 2014)

DNAlig1

Dlig-I

(Zhang et al., 2018)

DmDNA Lig I

(Easwaran et al., 2007)

LIG1

(Barclay et al., 2014)

Name Synonyms