Gene detail

Detailed information of OS493_024928-T1 in Lophelia pertusa

Genomic Location: scaffold_119:229053...231667
NR annotation: KAJ7357417.1, General transcription and DNA repair factor IIH helicase subunit XPD [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
A6QLJ0	General transcription and DNA repair factor IIH helicase subunit XPD OS=Bos taurus OX=9913 GN=ERCC2 PE=2 SV=1
Q60452	General transcription and DNA repair factor IIH helicase subunit XPD OS=Cricetulus griseus OX=10029 GN=ERCC2 PE=1 SV=1
P18074	General transcription and DNA repair factor IIH helicase subunit XPD OS=Homo sapiens OX=9606 GN=ERCC2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002859 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13307 all species →	Helicase_C_2	Helicase C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045028 all species →	Family	Helicase superfamily 1/2, DinG/Rad3-like	Interproscan
IPR006555 all species →	Domain	ATP-dependent helicase, C-terminal	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11472 all species →	DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003678 all species →	Molecular Function	DNA helicase activity	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006366 all species →	Biological Process	transcription by RNA polymerase II	Interproscan
GO:0045951 all species →	Biological Process	positive regulation of mitotic recombination	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0004386 all species →	Molecular Function	helicase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006139 all species →	Biological Process	nucleobase-containing compound metabolic process	Interproscan
GO:0016818 all species →	Molecular Function	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	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_024928-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_024928-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

107TPM > 0

7Conditions

20.4Max TPM

7.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	6.62	10.46
polyp at pH7 6	18	17	6.60	10.44
coral polyp · control treatment	16	16	7.98	20.43
coral polyp · oil and dispersant treatment	16	16	7.96	16.30
coral polyp · oil treatment	16	16	6.59	10.20
coral polyp · dispersant treatment	16	16	11.41	17.94
Polyp	10	9	7.59	13.42

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	-	10.46
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.61
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.80
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.28
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.92
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.74
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.05
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.60
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.46
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.27
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.08
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.81
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.94
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.77
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.96
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.44
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.49
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.70
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.46
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.04
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.99
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.92
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.84
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.43
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.84
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.75
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.56
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.35
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.21
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.31
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.43
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.04
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.25
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.17
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.57
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.85
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.40
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.05
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.99
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.46
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.46
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.23
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.05
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.32
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.30
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.87
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.24
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.71
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.08
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.06
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.94
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.51
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.17
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.56
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.50
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.17
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.92
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.85
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.19
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.56
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.13
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.37
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.43
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.33
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.93
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.90
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.75
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.66
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.77
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.18
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.71
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.02
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.63
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.94
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.57
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.49
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.43
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.21
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.66
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.01
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.60
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.66
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.49
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.40
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.86
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.04
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.17
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.28
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.82
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	13.42
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.72
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	9.95
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.18
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.49
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.60
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.75
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.56
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.17
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.