Gene detail

Detailed information of OS493_006387-T1 in Lophelia pertusa

Genomic Location: scaffold_13:2777241...2781243
NR annotation: KAJ7393414.1, DNA ligase 3 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

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
P0DOO3	DNA ligase OS=Variola virus (isolate Human/India/Ind3/1967) OX=587200 GN=OPG180 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003047 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00645 all species →	zf-PARP	Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region	Domain	Interproscan
PF04675 all species →	DNA_ligase_A_N	DNA ligase N terminus	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001510 all species →	Domain	Zinc finger, PARP-type	Interproscan
IPR036599 all species →	Homologous_superfamily	DNA ligase, ATP-dependent, N-terminal domain superfamily	Interproscan
IPR050191 all species →	Family	ATP-dependent DNA ligase	Interproscan
IPR036957 all species →	Homologous_superfamily	Zinc finger, PARP-type superfamily	Interproscan
IPR012308 all species →	Domain	DNA ligase, ATP-dependent, N-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:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003910 all species →	Molecular Function	DNA ligase (ATP) activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	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

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

No KEGG orthology assignment for OS493_006387-T1.

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_006387-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

108TPM > 0

7Conditions

14.8Max TPM

4.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.34	7.46
polyp at pH7 6	18	17	4.70	7.79
coral polyp · control treatment	16	16	6.14	14.80
coral polyp · oil and dispersant treatment	16	16	4.74	10.72
coral polyp · oil treatment	16	16	4.80	10.59
coral polyp · dispersant treatment	16	16	5.17	9.75
Polyp	10	9	1.88	5.05

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.46
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.57
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.60
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.54
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.13
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.13
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.03
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.63
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.13
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.89
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.82
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.60
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.45
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.45
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.25
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.85
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.20
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.38
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.21
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.90
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.89
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.70
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.57
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.46
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.30
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.18
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.94
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.55
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.54
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.51
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.33
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.04
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.30
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.80
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.65
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.25
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.56
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.36
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.22
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.96
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.36
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.30
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.05
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.56
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.21
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.78
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.69
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.50
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.34
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.26
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.75
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.64
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.56
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.30
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.19
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.14
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.58
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.55
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.41
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.32
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.96
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.90
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.59
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.49
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.41
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.24
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.23
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.88
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.09
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.90
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.24
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.02
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.79
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.06
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.57
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.49
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.72
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.75
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.53
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.51
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.99
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.88
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.65
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.63
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.57
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.12
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.54
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.33
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.52
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.82
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.82
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.66
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.05
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.23
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.36
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.16
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.14
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.09
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.74
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.59
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.48
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.