Gene detail

Detailed information of ENSKFPP00000027687.1 in Condylactis gigantea

Genomic Location: chr6:10233023...10240259
NR annotation: XP_031555591.1, DNA ligase 3-like [Actinia tenebrosa]
Species Condylactis gigantea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSKFPT00000030057

atggcggacgatTCTAAACCGTTTGTCGTAGAATACGCCTCTCAAGGTAGAGCAAAATGCAAGACTTGTAAACAACAGATTGAAAAGAAGTCTGCAAGAATAGGAAAACTTGTTACAAATCCTTTCAGTGAAGATGGAGGTACCATGAAACAGTGGTACCATGTTAAATGTATCTTTGAGGCTTTGAGTAGAGCTAGAGCAACGACGAGGAAGATCGAAACTACAAGTGATTTGGATGGATTTGAAGACatggatgatgacgacaagAACATGATTGAAGGCTTTATCAAAGGTATgggagggaagggaaggGCCTCTTCTACTTCAAAAAGTCCTGCTAATAAGAAGAAAGTTCAAGCAACTCTCAGTTTAAGCCCTACAAAAGGAACTGCTGTACGGACACTCACTACTGCTataAATAAACTGGATgcattgatattttttatcatgtACATATTGAAcacaaattcaaaaatcatGACTGTAAacaattcatttatttgtacGATTATGTGTATAGATGCTGCTGAACCATCCACAAGCAAGTATAGTTTAAGCAAGGATGACACATTTCGTGAGTTCAGACGTCTTTGTACCATGCTGGCAGGGGAACCAAGCTATAATGCCAAGACTAAGATCATTGCTGATTTCATAAACGCAGGAGCATCTGGAGATGAATACAATGGAGACTTGTTTCTGTTAGCCAAGCTGTTGTTACCAGGAGTAAACAAGAGAGTCtataatttacaaagcaaaCAGCTTATTAAGCTTTTCAGCCAGGTTTGTACATGTAGACATCATGGGGACGTAGCTGAGACCATAAGTGATTTCTTTGAGCAGAGCCTTGCTTGCAAACCAGTCAAGAAAAGTACACTGAGCAATCAAGAGGTTGATGAATTCCTGGATACTCTAACAACCTTCAGTAAAGAGGATGATCAGATGCGAGAATTACAAAAGATCACCAGAAAATGTACAGTTAATGACCTGAAATACATTATCCGACTCATCAAGCATGACCTTAGGATGAACACTGGTGCCAAGCATGTGTTAGAAGCCATTGATCCAGATGCCTACAAGGCATTCCAGGCATCAAATAACCTGAATGATGTAATCAAGAGATGCCTAGACAAAAGATCTGGAGATGGTGGTCATGGTGTACCATCCATGAAGAAGAAACTGAGCATTCGTGCCTCTGTGATGACACCCATCAAACCTATGCTGGCTGAAGCTTGCAAGTCCTTTGCACAAGCAATCAAGAAGAGCCCAGGTGGAATGTATGCTGAAATCAAGTATGATGGAGAGAGAGTCCAGGTCCATAAAAGTGGCCATAAGTTTGAGTTTTTCAGTCGTAACCTGAAACCTGTCACCCCCCACAAGGTTGCAGCCATAACAGACTTTCTTCCCAAAGCTTGTCCTCATGGAAACAACTTGATACTTGACAGTGAGGTTCTCCTCGTTGATAATAAAACTGGCACACCCCTTCCATTTGGAACTCTGGGGATTCACAAGAAATCAGCTTTTAAAGACGCAAGCGTATGTCTTTTCATATTCGACTGCATCCAgtttaatgatgaaaatgttatGACAAAGACCATGCAAGAAAGACGTCAGATTTTGGAGAAGAATGTGACTCCTATCAAGAACAGAATCATGCTCTCAGAAACTACTTTTGTCAAGACTGAAAAGGAGTTGTCCAAACTGATGGCCAGAGCTATGAGAGAAGGTCTGGAAGGTCTTGTTCTCAAAGATCTCAAGGGGTTGTACGAGCCTGGAAAACGACACTGGTTAAAGATGAAAAAGGACTACCTGGAAGAAGGTGCAATGGCAGATACTGCTGACCTGGTTGTTCTTGGCGCTTACTATGGTACTGGAAACAAAGGTGGGCTGATGTCTATATTCCTGATGGGTGTGTACAACCCCCGCACCAAGATGTGGTGTACAGTAGCGAAGTGTGGTAACGGCCATGATGATAAGACAATAGAGAGATTGAACAGAGaactgaagatgaagaaaataagCAAGGACCCCAACAGAGTTCCCACTTGGCTTGATATACACAGAAGTATCATTCCTGACTTTGTTGTGGATGACCCTAAGAAAGCACCGGTGTGGGAAATAACAGGAGCAGAGTTCAGCAAGTCAACAAAACACACCGCTAATGGGATATCAATACGATTCCCGAGGGTGACCCGCATAAGGGATGACAAGGATTGGGAGACCGCTACTGACCTCGACCATTTAGCGGTAACTCTTATTCATGATGACAACGAAGACTGTGAAGAAGAAACCGCTTCAACAAGTAAAGATGTGGACATGGATGATAAAGAAGATAACACTAAAAGCCcgggaaaaagaaaacgaaaagctGATTTGAATAATGACGAGGTCGAGAAGAAAGATTTGCCGTCTGTATTCGGTGGGCTACAGATTTTCGTGAGCGATGATATGAAGGACGCTAAGAAACTGAAACGTTACATCATTGCATATGATGGAGATATTGTTTCAGAATTAAACAAAGATACGGCTACACATATAGTGTGTAACAAAAAGGTTGGTAACACTATTGACGATTCTTAA

Transcript

ENSKFPT00000030057

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P49916	DNA ligase 3 OS=Homo sapiens OX=9606 GN=LIG3 PE=1 SV=2
P97386	DNA ligase 3 OS=Mus musculus OX=10090 GN=Lig3 PE=1 SV=2
Q67480	DNA ligase OS=Fowlpox virus (strain NVSL) OX=928301 GN=LIG PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003019 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04675 all species →	DNA_ligase_A_N	DNA ligase N terminus	Family	Interproscan
PF16759 all species →	LIG3_BRCT	DNA ligase 3 BRCT domain	Family	Interproscan
PF01068 all species →	DNA_ligase_A_M	ATP dependent DNA ligase domain	Domain	Interproscan
PF00645 all species →	zf-PARP	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region	Domain	Interproscan
PF04679 all species →	DNA_ligase_A_C	ATP dependent DNA ligase C terminal region	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050191 all species →	Family	ATP-dependent DNA ligase	Interproscan
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan
IPR012308 all species →	Domain	DNA ligase, ATP-dependent, N-terminal	Interproscan
IPR001510 all species →	Domain	Zinc finger, PARP-type	Interproscan
IPR016059 all species →	Conserved_site	DNA ligase, ATP-dependent, conserved site	Interproscan
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR036957 all species →	Homologous_superfamily	Zinc finger, PARP-type superfamily	Interproscan
IPR031916 all species →	Domain	DNA ligase 3, BRCT domain	Interproscan
IPR001357 all species →	Domain	BRCT domain	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR000977 all species →	Family	DNA ligase, ATP-dependent	Interproscan
IPR036599 all species →	Homologous_superfamily	DNA ligase, ATP-dependent, N-terminal domain superfamily	Interproscan
IPR012309 all species →	Domain	DNA ligase, ATP-dependent, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45674 all species →	DNA LIGASE 1/3 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003910 all species →	Molecular Function	DNA ligase (ATP) activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006266 all species →	Biological Process	DNA ligation	Interproscan
GO:0006273 all species →	Biological Process	lagging strand elongation	Interproscan
GO:0006288 all species →	Biological Process	base-excision repair, DNA ligation	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0070421 all species →	Cellular Component	DNA ligase III-XRCC1 complex	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003909 all species →	Molecular Function	DNA ligase activity	Interproscan
GO:0071897 all species →	Biological Process	DNA biosynthetic process	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K10776	LIG3; DNA ligase 3	EC:6.5.1.1	DNA repair and recombination proteins	ko03400	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Condylactis gigantea tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Condylactis gigantea, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →