Gene detail

Detailed information of OS493_004279-T1 in Lophelia pertusa

Genomic Location: scaffold_8:4493960...4500067
NR annotation: KAJ7387298.1, hypothetical protein OS493_004279 [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)	OG0001788 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for OS493_004279-T1 in Lophelia pertusa.

InterPro

InterPro term	Type	Description	Source
IPR006642 all species →	Domain	Rad18, zinc finger UBZ4-type	Interproscan
IPR038868 all species →	Family	BRCA1-A complex subunit RAP80	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15932 all species →	UBIQUITIN INTERACTION MOTIF-CONTAINING PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0042393 all species →	Molecular Function	histone binding	Interproscan
GO:0045739 all species →	Biological Process	positive regulation of DNA repair	Interproscan
GO:0070530 all species →	Molecular Function	K63-linked polyubiquitin modification-dependent protein binding	Interproscan
GO:0070531 all species →	Cellular Component	BRCA1-A 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_004279-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_004279-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

99TPM > 0

7Conditions

55.4Max TPM

2.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	1.80	4.20
polyp at pH7 6	18	17	1.85	4.66
coral polyp · control treatment	16	15	4.44	55.36
coral polyp · oil and dispersant treatment	16	14	3.61	46.71
coral polyp · oil treatment	16	15	1.22	4.52
coral polyp · dispersant treatment	16	15	1.32	3.71
Polyp	10	7	1.06	3.11

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.20
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.07
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.96
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.76
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.61
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.32
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.23
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.06
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.98
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.77
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.50
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.22
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.07
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.94
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.92
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.85
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.66
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.56
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.18
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.58
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.11
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.08
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.97
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.93
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.92
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.63
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.45
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.33
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.32
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.25
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.82
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.71
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.36
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.72
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.86
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.54
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.28
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.12
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.77
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.73
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.72
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.71
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.37
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.25
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.71
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.98
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.84
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.42
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.21
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.92
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.82
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.34
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.25
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.23
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.52
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.90
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.15
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.55
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.36
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.32
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.24
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.98
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.73
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.71
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.64
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.48
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.36
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.30
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.24
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.71
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.80
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.84
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.76
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.68
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.00
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.94
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.74
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.69
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.68
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.57
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.51
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.11
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.37
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.62
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.10
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.81
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.73
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.