Gene detail

Detailed information of OS493_019642-T1 in Lophelia pertusa

Genomic Location: scaffold_69:1576150...1592759
NR annotation: KAJ7378944.1, DNA ligase (ATP) [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
Q90YB1	DNA ligase 4 OS=Gallus gallus OX=9031 GN=LIG4 PE=2 SV=2
Q8BTF7	DNA ligase 4 OS=Mus musculus OX=10090 GN=Lig4 PE=2 SV=2
G3GTP0	DNA ligase 4 OS=Cricetulus griseus OX=10029 GN=LIG4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002928 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01068 all species →	DNA_ligase_A_M	ATP dependent DNA ligase domain	Domain	Interproscan
PF04679 all species →	DNA_ligase_A_C	ATP dependent DNA ligase C terminal region	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan
IPR029710 all species →	Family	DNA ligase 4	Interproscan
IPR012309 all species →	Domain	DNA ligase, ATP-dependent, C-terminal	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR044125 all species →	Domain	DNA Ligase 4, adenylation domain	Interproscan
IPR000977 all species →	Family	DNA ligase, ATP-dependent	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45997 all species →	DNA LIGASE 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003910 all species →	Molecular Function	DNA ligase (ATP) activity	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:0005958 all species →	Cellular Component	DNA-dependent protein kinase-DNA ligase 4 complex	Interproscan
GO:0006297 all species →	Biological Process	nucleotide-excision repair, DNA gap filling	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0032807 all species →	Cellular Component	DNA ligase IV complex	Interproscan
GO:0051103 all species →	Biological Process	DNA ligation involved in DNA repair	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

No KEGG orthology assignment for OS493_019642-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_019642-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

109TPM > 0

7Conditions

20.7Max TPM

8.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.99	13.40
polyp at pH7 6	18	17	8.45	15.77
coral polyp · control treatment	16	16	8.81	20.72
coral polyp · oil and dispersant treatment	16	16	6.77	13.62
coral polyp · oil treatment	16	16	9.27	16.81
coral polyp · dispersant treatment	16	16	6.67	11.71
Polyp	10	10	7.31	17.43

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	-	13.40
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.75
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.47
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.30
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.94
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.85
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.77
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.41
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.99
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.95
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.47
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.30
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.71
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.70
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.54
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.05
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.06
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.27
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.77
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.90
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.17
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.89
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.49
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.46
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.27
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.24
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.24
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.45
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.44
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.79
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.63
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.12
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.81
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.72
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.09
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.39
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.25
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.34
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.18
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.39
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.13
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.55
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.46
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.31
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.27
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.34
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.38
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.62
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.25
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.61
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.98
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.54
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.45
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.99
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.33
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.96
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.03
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.29
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.09
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.08
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.83
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.81
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.31
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.79
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.59
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.25
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.11
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.07
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.38
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.20
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.79
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.50
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.35
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.24
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.99
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.02
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.71
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.43
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.05
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.79
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.35
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.60
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.01
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.28
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.03
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.96
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.91
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.54
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.33
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.19
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.43
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.31
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.23
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.81
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.58
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.35
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.31
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.14
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.38

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.