Gene detail

Detailed information of OS493_024627-T1 in Lophelia pertusa

Genomic Location: scaffold_116:287168...287911
NR annotation: KAJ7383942.1, Endoribonuclease Dicer [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
Q9VCU9	Endoribonuclease Dcr-1 OS=Drosophila melanogaster OX=7227 GN=Dcr-1 PE=1 SV=1
Q6TV19	Endoribonuclease Dicer OS=Danio rerio OX=7955 GN=dicer1 PE=2 SV=2
P84634	Dicer-like protein 4 OS=Arabidopsis thaliana OX=3702 GN=DCL4 PE=1 SV=2

Gene family

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

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00636 all species →	Ribonuclease_3	Ribonuclease III domain	Family	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

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: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: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_024627-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_024627-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

63.5Max TPM

25.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.34	34.16
polyp at pH7 6	18	18	18.23	30.82
coral polyp · control treatment	16	16	34.03	55.95
coral polyp · oil and dispersant treatment	16	16	35.82	63.54
coral polyp · oil treatment	16	16	27.25	54.16
coral polyp · dispersant treatment	16	16	26.15	42.57
Polyp	10	10	8.84	17.15

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	-	34.16
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.84
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.84
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.80
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.73
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.71
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.25
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.38
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.40
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.10
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.13
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.21
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.79
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.47
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.39
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.34
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.26
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.82
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.39
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.78
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.11
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.24
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.88
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.69
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.65
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.71
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.87
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.86
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.81
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.89
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.68
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.26
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.60
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.44
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.86
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.59
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.46
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.49
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.19
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.40
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.24
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.41
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.96
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.62
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.75
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.35
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.94
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.85
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.54
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.25
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.26
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.74
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.89
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.84
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.67
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.85
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.59
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.65
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.60
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.42
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.91
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.76
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.35
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.76
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.16
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.18
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.32
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.73
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.63
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.21
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.29
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.08
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.51
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.11
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.50
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.91
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.46
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.58
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.73
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.57
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.57
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.02
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.43
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.79
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.65
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.41
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.81
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.13
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.52
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.14
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.59
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.19
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.44
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	17.15
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	13.10
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.84
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.77
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.88
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.19
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.16
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.84

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.