Gene detail

Detailed information of OS493_030988-T1 in Lophelia pertusa

Genomic Location: scaffold_207:225440...226921
NR annotation: KAJ7377030.1, Component of the BRCA1-A complex [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004334 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for OS493_030988-T1 in Lophelia pertusa.

InterPro

InterPro term	Type	Description	Source
IPR026126 all species →	Family	BRISC and BRCA1-A complex member 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15660 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0007095 all species →	Biological Process	mitotic G2 DNA damage checkpoint signaling	Interproscan
GO:0016604 all species →	Cellular Component	nuclear body	Interproscan
GO:0045739 all species →	Biological Process	positive regulation of DNA repair	Interproscan
GO:0070531 all species →	Cellular Component	BRCA1-A complex	Interproscan
GO:0070552 all species →	Cellular Component	BRISC 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_030988-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_030988-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

58.1Max TPM

13.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.69	36.10
polyp at pH7 6	18	16	16.15	25.34
coral polyp · control treatment	16	16	11.43	29.94
coral polyp · oil and dispersant treatment	16	15	10.56	58.13
coral polyp · oil treatment	16	16	11.03	16.37
coral polyp · dispersant treatment	16	16	8.17	13.64
Polyp	10	9	12.44	22.92

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	-	36.10
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.95
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.90
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.35
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.31
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.50
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.20
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.15
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.79
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.61
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.07
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.88
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.46
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.30
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.88
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.19
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.33
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.18
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.56
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.63
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.39
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.35
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.85
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.14
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.63
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.15
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.02
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.50
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.57
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.27
SRR11359513	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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.94
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.25
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.06
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.88
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.81
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.63
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.90
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.86
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.43
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.50
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.85
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.67
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.44
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.56
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.10
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.13
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.39
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.91
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.23
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.81
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.61
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.52
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.42
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.97
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.85
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.81
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.18
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.76
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.08
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.89
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.61
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.61
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.44
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.44
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.67
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.99
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.19
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.19
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.11
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.45
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.58
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.49
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.39
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.64
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.38
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.93
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.81
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.54
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.27
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.98
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.71
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.42
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.03
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.61
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.43
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.17
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.03
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	22.92
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	21.59
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	21.33
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	16.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	14.79
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.51
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.85
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.18
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.