Gene detail

Detailed information of OS493_017452-T1 in Lophelia pertusa

Genomic Location: scaffold_56:289019...301915
NR annotation: KAJ7385087.1, PAB-dependent poly(A)-specific ribonuclease subunit 3 [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
A1L1C7	PAN2-PAN3 deadenylation complex subunit pan3 OS=Xenopus tropicalis OX=8364 GN=pan3 PE=2 SV=1
Q640Q5	PAN2-PAN3 deadenylation complex subunit Pan3 OS=Mus musculus OX=10090 GN=Pan3 PE=1 SV=4
Q58A45	PAN2-PAN3 deadenylation complex subunit PAN3 OS=Homo sapiens OX=9606 GN=PAN3 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005429 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00642 all species →	zf-CCCH	Zinc finger C-x8-C-x5-C-x3-H type (and similar)	Family	Interproscan
PF18101 all species →	Pan3_PK	Pan3 Pseudokinase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000571 all species →	Domain	Zinc finger, CCCH-type	Interproscan
IPR041332 all species →	Domain	Pan3 pseudokinase domain	Interproscan
IPR030844 all species →	Family	PAN2-PAN3 deadenylation complex subunit PAN3	Interproscan
IPR036855 all species →	Homologous_superfamily	Zinc finger, CCCH-type superfamily	Interproscan
IPR011009 all species →	Homologous_superfamily	Protein kinase-like domain superfamily	Interproscan
IPR000719 all species →	Domain	Protein kinase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12272 all species →	DEADENYLATION COMPLEX SUBUNIT PAN3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0000289 all species →	Biological Process	nuclear-transcribed mRNA poly(A) tail shortening	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:0008143 all species →	Molecular Function	poly(A) binding	Interproscan
GO:0031251 all species →	Cellular Component	PAN complex	Interproscan
GO:0004672 all species →	Molecular Function	protein kinase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006468 all species →	Biological Process	protein phosphorylation	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_017452-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_017452-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

47.2Max TPM

18.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	24.24	47.22
polyp at pH7 6	18	18	20.26	37.79
coral polyp · control treatment	16	16	20.00	32.24
coral polyp · oil and dispersant treatment	16	16	15.12	30.00
coral polyp · oil treatment	16	16	22.67	36.62
coral polyp · dispersant treatment	16	16	12.44	23.17
Polyp	10	9	7.52	19.04

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	-	47.22
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.77
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.90
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.62
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.48
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.05
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.30
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.83
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.93
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.34
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.87
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.15
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.76
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.32
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.89
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.70
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.87
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.24
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.79
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.63
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.87
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.03
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.30
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.60
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.11
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.53
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.10
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.59
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.14
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.05
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.02
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.64
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.61
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.02
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.54
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.12
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.24
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.39
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.89
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.00
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.83
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.71
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.93
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.64
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.44
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.49
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.46
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.17
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.96
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.88
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.09
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.23
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.82
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.58
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.35
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.95
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.46
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.12
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.24
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.10
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.07
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.79
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.32
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.88
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.62
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.44
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.55
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.46
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.38
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.94
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.63
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.77
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.35
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.28
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.02
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.21
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.95
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.54
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.81
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.76
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.17
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.67
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.80
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.80
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.54
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.59
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.35
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.45
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.60
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.84
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.40
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.77
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.03
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.39
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.57
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	19.04
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	11.18
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.12
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.50
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.06
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.48
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.39
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.01
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.