Gene detail

Detailed information of OS493_018035-T1 in Lophelia pertusa

Genomic Location: scaffold_58:2001673...2008241
NR annotation: KAJ7372757.1, hypothetical protein OS493_018035 [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)	OG0009338 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00035 all species →	dsrm	Double-stranded RNA binding motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051247 all species →	Family	RISC Loading Complex Component	Interproscan
IPR014720 all species →	Domain	Double-stranded RNA-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46205 all species →	LOQUACIOUS, ISOFORM B	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003725 all species →	Molecular Function	double-stranded RNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0016442 all species →	Cellular Component	RISC complex	Interproscan
GO:0030422 all species →	Biological Process	siRNA processing	Interproscan
GO:0035197 all species →	Molecular Function	siRNA binding	Interproscan
GO:0070578 all species →	Cellular Component	RISC-loading complex	Interproscan
GO:0070920 all species →	Biological Process	regulation of regulatory ncRNA processing	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
K18420	TARBP2; RISC-loading complex subunit TARBP2	-	Chromosome and associated proteins	ko03036	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_018035-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

110TPM > 0

7Conditions

164.7Max TPM

47.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	29.43	45.32
polyp at pH7 6	18	18	28.45	39.24
coral polyp · control treatment	16	16	53.11	127.56
coral polyp · oil and dispersant treatment	16	16	58.44	112.81
coral polyp · oil treatment	16	16	58.29	164.74
coral polyp · dispersant treatment	16	16	64.66	132.93
Polyp	10	10	38.83	67.54

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.32
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.76
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.38
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.56
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.46
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.72
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.08
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.03
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.99
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.19
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.06
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.25
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.07
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.53
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.08
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.55
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.64
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.05
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.24
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.06
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.69
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.77
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.03
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.31
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.50
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.66
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.77
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.09
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.91
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.36
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.48
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.40
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.26
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.66
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.79
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	127.56
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.17
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.44
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.26
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.57
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.71
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.12
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.09
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.45
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.43
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.26
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.21
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.10
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.93
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.88
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.81
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	102.61
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.79
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.02
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.87
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.83
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.04
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.51
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.58
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.62
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.98
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.82
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.80
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.33
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.62
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	164.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.91
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.92
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.80
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.24
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.59
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.12
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.69
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.53
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.13
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.09
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.65
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.71
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.32
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.26
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	132.93
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	110.75
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	88.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.10
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.65
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.09
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.79
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.15
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.03
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.71
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.09
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.99
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.48
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.40
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	67.54
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	48.26
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	41.97
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	39.17
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	38.73
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	33.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	33.26
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	32.08
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	29.79
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	23.90

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.