Gene detail

Detailed information of OS493_024621-T1 in Lophelia pertusa

Genomic Location: scaffold_116:244207...245608
NR annotation: KAJ7383936.1, hypothetical protein OS493_024621 [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
Q6TV19	Endoribonuclease Dicer OS=Danio rerio OX=7955 GN=dicer1 PE=2 SV=2
Q25BN1	Endoribonuclease Dicer OS=Gallus gallus OX=9031 GN=DICER1 PE=2 SV=3
Q9UPY3	Endoribonuclease Dicer OS=Homo sapiens OX=9606 GN=DICER1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001530 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF20932 all species →	Dicer_dsRBD	Dicer, dsRNA-binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036389 all species →	Homologous_superfamily	Ribonuclease III, endonuclease domain superfamily	Interproscan
IPR000999 all species →	Domain	Ribonuclease III domain	Interproscan
IPR044441 all species →	Domain	Dicer, double-stranded RNA-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14950 all species →	DICER-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004525 all species →	Molecular Function	ribonuclease III activity	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004530 all species →	Molecular Function	deoxyribonuclease I activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006309 all species →	Biological Process	apoptotic DNA fragmentation	Interproscan
GO:0016442 all species →	Cellular Component	RISC complex	Interproscan
GO:0030422 all species →	Biological Process	siRNA processing	Interproscan
GO:0031054 all species →	Biological Process	pre-miRNA processing	Interproscan
GO:0090501 all species →	Biological Process	obsolete RNA phosphodiester bond hydrolysis	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_024621-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_024621-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

107TPM > 0

7Conditions

38.7Max TPM

12.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	20.61	32.81
polyp at pH7 6	18	17	17.90	38.69
coral polyp · control treatment	16	16	9.36	17.32
coral polyp · oil and dispersant treatment	16	16	11.16	18.47
coral polyp · oil treatment	16	16	8.12	12.45
coral polyp · dispersant treatment	16	16	6.46	12.83
Polyp	10	9	6.39	11.47

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.81
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.63
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.41
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.88
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.77
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.41
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.86
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.58
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.53
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.28
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.26
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.42
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.10
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.88
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.47
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.35
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.33
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.69
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.33
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.75
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.85
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.32
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.85
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.48
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.46
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.24
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.12
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.74
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.08
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.74
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.39
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.93
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.71
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.44
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.32
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.75
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.09
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.42
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.57
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.32
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.65
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.85
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.88
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.76
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.96
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.73
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.97
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.26
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.61
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.47
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.13
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.14
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.71
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.57
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.63
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.30
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.17
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.15
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.85
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.71
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.34
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.55
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.97
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.45
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.91
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.89
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.97
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.62
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.31
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.98
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.58
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.87
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.51
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.85
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.40
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.20
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.83
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.83
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.40
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.06
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.01
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.01
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.48
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.55
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.60
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.09
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.99
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.60
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.30
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.44
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.91
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.47
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.73
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.30
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.97
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.03
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.83
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.96
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.