Gene detail

Detailed information of OS493_040202-T1 in Lophelia pertusa

Genomic Location: scaffold_1869:4894...10935
NR annotation: KAJ7375588.1, DNA repair protein xrcc4 [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
Q924T3	DNA repair protein XRCC4 OS=Mus musculus OX=10090 GN=Xrcc4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006671 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06632 all species →	XRCC4	DNA double-strand break repair and V(D)J recombination protein XRCC4	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR010585 all species →	Family	DNA repair protein XRCC4	Interproscan
IPR014751 all species →	Homologous_superfamily	DNA repair protein XRCC4-like, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR28559 all species →	DNA REPAIR PROTEIN XRCC4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0005958 all species →	Cellular Component	DNA-dependent protein kinase-DNA ligase 4 complex	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0010165 all species →	Biological Process	response to X-ray	Interproscan
GO:0032807 all species →	Cellular Component	DNA ligase IV complex	Interproscan
GO:0051103 all species →	Biological Process	DNA ligation involved in DNA repair	Interproscan
GO:0051351 all species →	Biological Process	positive regulation of ligase activity	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_040202-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_040202-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

97TPM > 0

7Conditions

16.3Max TPM

3.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	14	4.19	8.92
polyp at pH7 6	18	12	3.28	6.58
coral polyp · control treatment	16	16	2.87	5.89
coral polyp · oil and dispersant treatment	16	16	2.16	13.21
coral polyp · oil treatment	16	16	3.04	5.17
coral polyp · dispersant treatment	16	14	1.55	4.69
Polyp	10	9	6.80	16.32

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	-	8.92
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.04
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.91
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.89
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.70
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.83
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.06
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.56
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.39
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.91
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.20
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.49
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	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
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.58
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.46
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.30
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.13
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.47
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.44
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.42
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.47
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.31
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.72
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.79
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.94
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	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
SRR11359517	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
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.89
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.51
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.43
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.95
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.71
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.21
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.85
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.79
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.21
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.18
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.86
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.67
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.66
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.34
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.84
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.21
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.80
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.72
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.42
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.02
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.40
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.39
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.06
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.02
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.99
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.72
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.52
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.17
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.96
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.39
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.35
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.11
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.64
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.53
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.22
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.81
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.47
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.98
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.77
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.43
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.20
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.69
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.96
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.82
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.15
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.92
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.70
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.68
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.47
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.10
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.06
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.79
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.65
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.49
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	-	16.32
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.66
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.84
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.69
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.65
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.34
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.97
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.87
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.64
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.