Gene detail

Detailed information of OS493_003238-T1 in Lophelia pertusa

Genomic Location: scaffold_6:6765212...6772210
NR annotation: KAJ7340488.1, DNA topoisomerase 3-alpha [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
O70157	DNA topoisomerase 3-alpha OS=Mus musculus OX=10090 GN=Top3a PE=2 SV=1
Q13472	DNA topoisomerase 3-alpha OS=Homo sapiens OX=9606 GN=TOP3A PE=1 SV=1
Q9NG98	DNA topoisomerase 3-alpha OS=Drosophila melanogaster OX=7227 GN=Top3alpha PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003263 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01131 all species →	Topoisom_bac	DNA topoisomerase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR023406 all species →	Active_site	DNA topoisomerase, type IA, active site	Interproscan
IPR000380 all species →	Family	DNA topoisomerase, type IA	Interproscan
IPR013497 all species →	Domain	DNA topoisomerase, type IA, central	Interproscan
IPR003602 all species →	Domain	DNA topoisomerase, type IA, DNA-binding domain	Interproscan
IPR023405 all species →	Homologous_superfamily	DNA topoisomerase, type IA, core domain	Interproscan
IPR013825 all species →	Homologous_superfamily	DNA topoisomerase, type IA, central region, subdomain 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11390 all species →	PROKARYOTIC DNA TOPOISOMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003917 all species →	Molecular Function	DNA topoisomerase type I (single strand cut, ATP-independent) activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003916 all species →	Molecular Function	DNA topoisomerase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006265 all species →	Biological Process	DNA topological change	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_003238-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_003238-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

103TPM > 0

7Conditions

84.5Max TPM

4.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	3.81	6.59
polyp at pH7 6	18	14	2.79	6.33
coral polyp · control treatment	16	16	7.39	66.48
coral polyp · oil and dispersant treatment	16	16	7.34	84.55
coral polyp · oil treatment	16	16	3.94	6.39
coral polyp · dispersant treatment	16	16	2.57	4.52
Polyp	10	9	2.05	4.25

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.59
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.88
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.35
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.08
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.06
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.77
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.77
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.61
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.58
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.24
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.13
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.03
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.60
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.36
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.02
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.33
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.21
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.79
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.49
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.98
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.29
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.23
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.71
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.55
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.29
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.92
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
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	66.48
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.10
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.71
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.66
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.12
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.59
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.48
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.96
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.84
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.20
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.09
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.04
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.51
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.55
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.66
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.50
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.73
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.30
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.26
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.26
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.16
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.91
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.83
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.83
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.17
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.75
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.64
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.39
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.38
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.65
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.61
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.51
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.23
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.14
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.47
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.46
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.71
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.23
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.52
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.28
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.06
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.72
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.47
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.84
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.76
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.41
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.40
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.01
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.82
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.20
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.17
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.25
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.36
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.63
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.47
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.63
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.43
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.03
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.72
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.