Gene detail

Detailed information of OS493_029850-T1 in Lophelia pertusa

Genomic Location: scaffold_185:541286...550913
NR annotation: KAJ7354844.1, DNA topoisomerase 2-beta [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
O42131	DNA topoisomerase 2-beta OS=Gallus gallus OX=9031 GN=TOP2B PE=2 SV=1
P41515	DNA topoisomerase 2-alpha OS=Cricetulus griseus OX=10029 GN=TOP2A PE=2 SV=1
O46374	DNA topoisomerase 2-alpha OS=Sus scrofa OX=9823 GN=TOP2A PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002381 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00521 all species →	DNA_topoisoIV	DNA gyrase/topoisomerase IV, subunit A	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013757 all species →	Homologous_superfamily	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Interproscan
IPR002205 all species →	Domain	DNA topoisomerase, type IIA, domain A	Interproscan
IPR050634 all species →	Family	DNA Topoisomerase II Enzyme	Interproscan
IPR013758 all species →	Homologous_superfamily	DNA topoisomerase, type IIA, domain A, alpha-beta	Interproscan
IPR013760 all species →	Homologous_superfamily	DNA topoisomerase, type IIA-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10169 all species →	DNA TOPOISOMERASE/GYRASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003918 all species →	Molecular Function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006265 all species →	Biological Process	DNA topological change	Interproscan
GO:0000712 all species →	Biological Process	resolution of meiotic recombination intermediates	Interproscan
GO:0000819 all species →	Biological Process	sister chromatid segregation	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006259 all species →	Biological Process	DNA metabolic 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_029850-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_029850-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

110TPM > 0

7Conditions

149.5Max TPM

15.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.25	22.61
polyp at pH7 6	18	18	12.71	25.89
coral polyp · control treatment	16	16	22.79	149.53
coral polyp · oil and dispersant treatment	16	16	17.98	138.87
coral polyp · oil treatment	16	16	14.60	28.92
coral polyp · dispersant treatment	16	16	12.30	21.15
Polyp	10	10	12.26	31.18

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	-	22.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.74
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.62
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.27
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.28
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.03
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.13
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.83
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.77
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.85
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.07
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.06
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.46
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.46
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.29
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.69
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.48
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.91
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.89
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.79
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.09
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.38
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.27
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.62
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.18
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.82
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.47
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.88
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.70
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.63
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.17
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.79
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.41
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.31
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.14
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	149.53
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.99
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.37
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.88
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.81
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.38
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.50
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.20
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.57
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.48
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.14
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.62
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.15
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.11
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.78
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.11
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	138.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.93
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.86
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.64
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.41
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.32
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.28
SRR16705945	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	8.49
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.40
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.14
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.67
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.34
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.51
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.86
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.92
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.84
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.80
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.25
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.26
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.05
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.52
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.73
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.65
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.54
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.50
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.55
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.78
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.71
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.84
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.69
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.15
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.03
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.51
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.67
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.13
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.30
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.01
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.76
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.31
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.16
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.50
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.28
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.02
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.73
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.91
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	31.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	12.92
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.12
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	11.04
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.16
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.54
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	9.29
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.17
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.16

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.