Gene detail

Detailed information of OS493_023732-T1 in Lophelia pertusa

Genomic Location: scaffold_106:1015301...1034160
NR annotation: KAJ7371701.1, hypothetical protein OS493_023732, partial [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
Q2HJ92	Interferon-inducible double-stranded RNA-dependent protein kinase activator A OS=Bos taurus OX=9913 GN=PRKRA PE=2 SV=1
O75569	Interferon-inducible double-stranded RNA-dependent protein kinase activator A OS=Homo sapiens OX=9606 GN=PRKRA PE=1 SV=1
Q9WTX2	Interferon-inducible double-stranded RNA-dependent protein kinase activator A OS=Mus musculus OX=10090 GN=Prkra PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002781 (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
IPR014720 all species →	Domain	Double-stranded RNA-binding domain	Interproscan
IPR051247 all species →	Family	RISC Loading Complex Component	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_023732-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

109TPM > 0

7Conditions

24.7Max TPM

13.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.70	18.37
polyp at pH7 6	18	18	14.41	22.06
coral polyp · control treatment	16	16	16.22	24.70
coral polyp · oil and dispersant treatment	16	16	11.15	19.14
coral polyp · oil treatment	16	16	14.91	22.47
coral polyp · dispersant treatment	16	16	10.43	21.87
Polyp	10	9	11.32	19.72

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.37
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.46
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.45
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.10
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.11
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.25
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.22
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.70
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.50
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.13
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.73
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.12
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.93
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.71
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.49
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.19
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.10
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.88
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.22
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.17
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.16
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.61
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.50
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.05
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.06
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.32
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.26
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.99
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.60
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.31
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.92
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.86
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.70
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.49
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.02
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.61
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.86
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.68
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.42
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.90
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.08
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.49
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.29
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.05
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.73
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.35
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.10
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.76
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.14
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.34
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.02
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.08
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.74
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.63
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.50
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.32
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.83
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.83
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.01
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.01
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.54
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.35
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.10
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.90
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.47
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.46
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.55
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.14
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.13
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.28
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.18
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.48
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.50
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.90
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.72
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.26
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.78
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.14
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.87
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.02
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.72
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.79
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.74
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.46
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.29
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.26
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.44
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.49
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.16
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.68
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.17
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.14
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.88
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	19.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.04
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.38
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	12.97
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.44
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.26
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.97
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.54
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.