Gene detail

Detailed information of OS493_011575-T1 in Lophelia pertusa

Genomic Location: scaffold_29:2665708...2672854
NR annotation: KAJ7363291.1, DNA repair protein rad52 [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
P39022	DNA repair protein RAD52 homolog OS=Gallus gallus OX=9031 GN=RAD52 PE=2 SV=1
P43351	DNA repair protein RAD52 homolog OS=Homo sapiens OX=9606 GN=RAD52 PE=1 SV=1
P43352	DNA repair protein RAD52 homolog OS=Mus musculus OX=10090 GN=Rad52 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008844 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04098 all species →	Rad52_Rad22	Rad52/22 family double-strand break repair protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR042525 all species →	Homologous_superfamily	DNA repair protein Rad52/59/22 superfamily	Interproscan
IPR041247 all species →	Family	Rad52 family	Interproscan
IPR004585 all species →	Family	DNA recombination/repair protein Rad52	Interproscan
IPR007232 all species →	Family	DNA repair protein Rad52/59/22	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12132 all species →	DNA REPAIR AND RECOMBINATION PROTEIN RAD52, RAD59	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0000730 all species →	Biological Process	DNA recombinase assembly	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0045002 all species →	Biological Process	double-strand break repair via single-strand annealing	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0006312 all species →	Biological Process	mitotic recombination	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
K10873	RAD52; DNA repair and recombination protein RAD52	-	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_011575-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

104TPM > 0

7Conditions

12.6Max TPM

1.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	2.55	6.29
polyp at pH7 6	18	15	2.16	5.79
coral polyp · control treatment	16	16	1.65	12.58
coral polyp · oil and dispersant treatment	16	16	1.20	9.20
coral polyp · oil treatment	16	16	1.49	3.04
coral polyp · dispersant treatment	16	15	0.66	1.91
Polyp	10	9	1.29	2.38

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.29
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.56
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.52
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.21
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.58
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.55
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.39
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.32
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.17
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.10
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.09
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.02
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.87
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.71
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.62
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.59
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.35
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.79
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.26
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.53
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.17
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.22
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.16
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.81
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.73
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.48
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.10
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.94
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.91
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
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.58
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.59
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.53
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.39
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.19
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.15
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.15
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.94
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.64
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.61
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.55
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.43
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.39
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.30
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.16
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.20
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.37
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.32
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.26
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.77
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.64
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.56
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.47
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.44
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.38
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.37
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.34
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.27
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.14
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.04
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.46
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.95
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.76
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.67
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.51
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.47
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.41
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.26
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.19
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.13
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.75
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.54
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.52
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.29
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.19
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.95
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.94
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.81
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.67
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.46
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.41
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.40
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.37
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.15
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.14
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.38
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.28
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.93
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.91
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.63
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.18
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.92
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.38
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.29
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.