Gene detail

Detailed information of OS493_004055-T1 in Lophelia pertusa

Genomic Location: scaffold_8:1844196...1848914
NR annotation: KAJ7387091.1, DNA repair protein rad51c [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
Q8R2J9	DNA repair protein RAD51 homolog 3 OS=Cricetulus griseus OX=10029 GN=RAD51C PE=2 SV=1
Q924H5	DNA repair protein RAD51 homolog 3 OS=Mus musculus OX=10090 GN=Rad51c PE=1 SV=1
O43502	DNA repair protein RAD51 homolog 3 OS=Homo sapiens OX=9606 GN=RAD51C PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006197 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08423 all species →	Rad51	Rad51	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR020588 all species →	Domain	DNA recombination and repair protein RecA-like, ATP-binding domain	Interproscan
IPR052093 all species →	Family	Homologous Recombination Repair Mediator	Interproscan
IPR013632 all species →	Domain	DNA recombination and repair protein Rad51-like, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46239 all species →	DNA REPAIR PROTEIN RAD51 HOMOLOG 3 RAD51C	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor activity	Interproscan
GO:0000400 all species →	Molecular Function	four-way junction DNA binding	Interproscan
GO:0000707 all species →	Biological Process	meiotic DNA recombinase assembly	Interproscan
GO:0005657 all species →	Cellular Component	replication fork	Interproscan
GO:0007131 all species →	Biological Process	reciprocal meiotic recombination	Interproscan
GO:0008821 all species →	Molecular Function	crossover junction DNA endonuclease activity	Interproscan
GO:0033063 all species →	Cellular Component	Rad51B-Rad51C-Rad51D-XRCC2 complex	Interproscan
GO:0033065 all species →	Cellular Component	Rad51C-XRCC3 complex	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_004055-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_004055-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

106TPM > 0

7Conditions

51.7Max TPM

5.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.16	14.96
polyp at pH7 6	18	17	5.92	10.17
coral polyp · control treatment	16	16	8.38	51.74
coral polyp · oil and dispersant treatment	16	16	5.17	23.32
coral polyp · oil treatment	16	16	6.62	18.22
coral polyp · dispersant treatment	16	15	2.75	7.01
Polyp	10	8	5.15	14.75

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.88
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.29
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.19
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.57
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.36
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.46
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.10
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.94
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.74
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.35
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.73
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.65
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.63
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.47
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.32
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.10
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.09
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.17
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.58
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.93
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.51
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.79
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.90
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.45
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.35
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.26
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.72
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.68
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.44
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.43
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.27
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.13
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.73
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.29
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.90
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.89
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.97
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.68
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.24
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.00
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.96
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.59
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.80
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.64
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.51
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.88
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.78
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.32
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.02
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.81
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.68
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.89
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.60
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.29
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.21
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.39
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.73
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.72
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.47
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.84
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.61
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.22
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.96
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.53
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.95
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.81
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.53
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.47
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.06
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.93
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.25
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.30
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.74
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.58
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.67
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.54
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.01
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.05
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.88
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.37
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.21
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.15
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.92
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.91
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.69
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.44
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.08
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.95
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.88
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.27
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.24
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.75
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.57
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.28
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.74
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.89
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.83
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.18
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
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.