Gene detail

Detailed information of OS493_019016-T1 in Lophelia pertusa

Genomic Location: scaffold_64:1273781...1282268
NR annotation: KAJ7372507.1, 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
Q13426	DNA repair protein XRCC4 OS=Homo sapiens OX=9606 GN=XRCC4 PE=1 SV=2

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
IPR038051 all species →	Homologous_superfamily	XRCC4-like, N-terminal domain superfamily	Interproscan
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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K10886	XRCC4; DNA-repair protein XRCC4	-	DNA repair and recombination proteins	ko03400	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_019016-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

36.8Max TPM

7.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.57	13.01
polyp at pH7 6	18	18	8.85	14.40
coral polyp · control treatment	16	16	6.48	12.13
coral polyp · oil and dispersant treatment	16	16	3.49	9.83
coral polyp · oil treatment	16	16	7.17	11.04
coral polyp · dispersant treatment	16	16	3.75	7.39
Polyp	10	10	11.78	36.77

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.01
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.54
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.39
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.22
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.84
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.71
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.51
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.38
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.19
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.47
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.41
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.38
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.29
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.78
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.73
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.61
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.01
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.40
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.29
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.22
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.03
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.16
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.05
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.50
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.49
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.78
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.75
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.71
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.66
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.63
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.01
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.92
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.14
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.01
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.51
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.13
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.44
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.05
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.89
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.04
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.47
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.88
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.68
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.32
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.97
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.67
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.15
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.11
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.72
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.43
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.83
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.98
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.66
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.36
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.33
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.89
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.55
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.01
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.57
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.50
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.18
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.16
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.72
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.04
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.93
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.51
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.30
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.14
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.07
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.59
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.91
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.58
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.55
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.41
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.02
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.84
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.49
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.15
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.18
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.39
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.85
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.92
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.20
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.91
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.65
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.82
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.79
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.53
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.11
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.08
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.81
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.50
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.86
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	36.77
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.92
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.46
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.06
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.63
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.85
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.49
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.54
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.06

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.