Gene detail

Detailed information of OS493_010644-T1 in Lophelia pertusa

Genomic Location: scaffold_26:1272138...1272308
NR annotation: KAJ7386244.1, tRNA ligase, partial [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
Q9W1H4	DNA ligase 1 OS=Drosophila melanogaster OX=7227 GN=DNAlig1 PE=1 SV=2
P51892	DNA ligase 1 OS=Xenopus laevis OX=8355 GN=lig1 PE=2 SV=1
P37913	DNA ligase 1 OS=Mus musculus OX=10090 GN=Lig1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003742 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_010644-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan
IPR050191 all species →	Family	ATP-dependent DNA ligase	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: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:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006266 all species →	Biological Process	DNA ligation	Interproscan
GO:0006273 all species →	Biological Process	lagging strand elongation	Interproscan
GO:1903461 all species →	Biological Process	Okazaki fragment processing involved in mitotic DNA replication	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_010644-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_010644-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

100TPM > 0

7Conditions

12.2Max TPM

2.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2.81	6.92
polyp at pH7 6	18	16	2.25	5.00
coral polyp · control treatment	16	15	3.01	7.58
coral polyp · oil and dispersant treatment	16	13	1.50	5.94
coral polyp · oil treatment	16	15	2.89	7.97
coral polyp · dispersant treatment	16	14	1.27	2.62
Polyp	10	9	2.45	12.17

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.92
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.64
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.42
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.14
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.08
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.96
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.72
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.71
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.42
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.40
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.36
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.06
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.75
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.42
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.34
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.32
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.42
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.27
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.84
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.03
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.62
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.29
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.21
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.09
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.53
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.28
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.16
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.08
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.83
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.74
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.58
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.40
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.25
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.76
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.52
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.14
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.92
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.57
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.44
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.29
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.10
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.38
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.09
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.94
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.94
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.62
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.48
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.28
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.10
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.41
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.26
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.95
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.84
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.79
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.27
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.23
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.97
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.45
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.08
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.35
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.32
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.42
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.98
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.82
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.77
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.70
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.66
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.52
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.48
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.37
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.97
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.97
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.52
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.45
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.28
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.09
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.61
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.27
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.12
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.17
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.91
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.04
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.87
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.53
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.42
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.38
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.20
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.01
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.