Gene detail

Detailed information of OS493_029221-T1 in Lophelia pertusa

Genomic Location: scaffold_175:690688...700872
NR annotation: KAJ7389796.1, DNA repair protein RAD51 [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
O15315	DNA repair protein RAD51 homolog 2 OS=Homo sapiens OX=9606 GN=RAD51B PE=1 SV=2
O35719	DNA repair protein RAD51 homolog 2 OS=Mus musculus OX=10090 GN=Rad51b PE=2 SV=2
Q9SK02	DNA repair protein RAD51 homolog 2 OS=Arabidopsis thaliana OX=3702 GN=RAD51B PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007363 (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
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR030548 all species →	Family	DNA repair protein RAD51 homologue 2	Interproscan
IPR020588 all species →	Domain	DNA recombination and repair protein RecA-like, ATP-binding domain	Interproscan
IPR013632 all species →	Domain	DNA recombination and repair protein Rad51-like, C-terminal	Interproscan
IPR016467 all species →	Family	DNA recombination and repair protein, RecA-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46456 all species →	DNA REPAIR PROTEIN RAD51 HOMOLOG 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0000400 all species →	Molecular Function	four-way junction DNA binding	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003690 all species →	Molecular Function	double-stranded DNA binding	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005657 all species →	Cellular Component	replication fork	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0008094 all species →	Molecular Function	ATP-dependent activity, acting on DNA	Interproscan
GO:0033063 all species →	Cellular Component	Rad51B-Rad51C-Rad51D-XRCC2 complex	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor 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
K10869	RAD51L1, RAD51B; RAD51-like protein 1	-	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_029221-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

109TPM > 0

7Conditions

25.5Max TPM

8.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.90	14.41
polyp at pH7 6	18	17	9.57	14.88
coral polyp · control treatment	16	16	11.29	25.53
coral polyp · oil and dispersant treatment	16	16	7.76	23.81
coral polyp · oil treatment	16	16	10.68	15.65
coral polyp · dispersant treatment	16	16	4.79	9.66
Polyp	10	10	8.18	18.06

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.41
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.57
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.37
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.02
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.99
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.72
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.99
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.79
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.77
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.65
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.49
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.13
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.98
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.79
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.63
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.17
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.99
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.70
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.88
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.18
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.86
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.54
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.40
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.95
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.23
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.92
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.57
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.88
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.77
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.59
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.25
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.79
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.28
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.57
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.53
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.31
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.80
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.23
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.01
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.38
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.16
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.29
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.49
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.47
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.66
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.65
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.02
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.94
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.81
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.15
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.91
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.01
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.35
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.02
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.74
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.86
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.18
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.30
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.20
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.94
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.90
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.51
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.38
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.83
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.65
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.38
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.33
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.88
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.74
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.65
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.37
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.87
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.65
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.56
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.17
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.62
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.58
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.36
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.66
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.49
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.01
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.16
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.77
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.64
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.94
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.75
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.51
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.81
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.58
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.37
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.04
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.47
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	18.06
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.48
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.44
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.53
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.29
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.59
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.86
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.04
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.19
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.28

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.