Gene detail

Detailed information of OS493_017453-T1 in Lophelia pertusa

Genomic Location: scaffold_56:302026...303072
NR annotation: KAJ7385088.1, 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
Q58A45	PAN2-PAN3 deadenylation complex subunit PAN3 OS=Homo sapiens OX=9606 GN=PAN3 PE=1 SV=3
Q640Q5	PAN2-PAN3 deadenylation complex subunit Pan3 OS=Mus musculus OX=10090 GN=Pan3 PE=1 SV=4
A1L1C7	PAN2-PAN3 deadenylation complex subunit pan3 OS=Xenopus tropicalis OX=8364 GN=pan3 PE=2 SV=1

Gene family

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

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18101 all species →	Pan3_PK	Pan3 Pseudokinase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR030844 all species →	Family	PAN2-PAN3 deadenylation complex subunit PAN3	Interproscan
IPR041332 all species →	Domain	Pan3 pseudokinase domain	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
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

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_017453-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_017453-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

108TPM > 0

7Conditions

71.9Max TPM

25.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	32.59	71.94
polyp at pH7 6	18	18	25.70	62.40
coral polyp · control treatment	16	16	30.42	44.17
coral polyp · oil and dispersant treatment	16	15	21.51	49.98
coral polyp · oil treatment	16	16	34.58	52.61
coral polyp · dispersant treatment	16	16	17.20	36.94
Polyp	10	9	12.50	24.08

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	-	71.94
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.10
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.51
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.95
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.80
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.02
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.96
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.10
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.07
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.10
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.86
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.22
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.91
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.20
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.11
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.40
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.28
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.72
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.05
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.40
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.39
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.14
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.54
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.52
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.12
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.71
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.37
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.90
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.48
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.76
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.48
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.36
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.17
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.68
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.29
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.48
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.13
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.70
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.67
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.44
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.85
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.54
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.66
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.64
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.40
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.53
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.98
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.31
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.26
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.50
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.14
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.94
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.75
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.73
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.85
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.81
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.40
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.36
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.61
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.47
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.28
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.40
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.55
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.22
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.70
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.68
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.44
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.05
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.85
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.36
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.07
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.84
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.05
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.94
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.50
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.13
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.34
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.21
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.17
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.87
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.08
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.18
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.89
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.51
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.51
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.81
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.41
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	24.08
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	22.04
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	18.91
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	14.86
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.44
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.86
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.77
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.95
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.