Gene detail

Detailed information of OS493_003239-T1 in Lophelia pertusa

Genomic Location: scaffold_6:6772691...6777662
NR annotation: KAJ7340489.1, hypothetical protein OS493_003239 [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
C7J0A2	DNA topoisomerase 3-alpha OS=Oryza sativa subsp. japonica OX=39947 GN=TOP3A PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003217 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01396 all species →	zf-C4_Topoisom	Topoisomerase DNA binding C4 zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013824 all species →	Homologous_superfamily	DNA topoisomerase, type IA, central region, subdomain 1	Interproscan
IPR000380 all species →	Family	DNA topoisomerase, type IA	Interproscan
IPR013498 all species →	Domain	DNA topoisomerase, type IA, zn finger	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003916 all species →	Molecular Function	DNA topoisomerase activity	Interproscan
GO:0003917 all species →	Molecular Function	DNA topoisomerase type I (single strand cut, ATP-independent) activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006265 all species →	Biological Process	DNA topological change	Interproscan
GO:0005694 all species →	Cellular Component	chromosome	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_003239-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_003239-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

105TPM > 0

7Conditions

53.8Max TPM

3.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	3.49	7.36
polyp at pH7 6	18	16	3.32	6.63
coral polyp · control treatment	16	16	6.41	53.85
coral polyp · oil and dispersant treatment	16	16	3.59	26.69
coral polyp · oil treatment	16	16	3.11	6.55
coral polyp · dispersant treatment	16	15	1.98	3.85
Polyp	10	9	2.82	5.58

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.36
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.29
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.24
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.72
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.95
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.85
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.59
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.30
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.04
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.68
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.48
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.46
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.27
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.66
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.43
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.34
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.63
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.01
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.84
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.59
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.57
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.19
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.94
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.45
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.44
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.36
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.17
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.75
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.53
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.62
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.71
SRR11359501	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	53.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.99
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.37
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.72
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.34
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.02
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.97
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.37
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.09
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.31
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.01
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.70
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.69
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.60
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.72
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.69
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.40
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.37
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.18
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.83
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.47
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.09
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.80
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.75
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.71
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.68
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.67
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.63
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.12
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.04
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.02
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.55
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.15
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.37
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.23
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.88
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.34
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.10
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.56
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.26
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.49
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.49
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.18
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.01
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.85
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.27
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.72
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.71
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.40
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.27
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.86
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.85
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.55
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.49
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.48
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.18
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.02
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.30
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.58
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.56
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.49
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.69
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.33
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.23
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.03
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.84
SRR7746667	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.