Gene detail

Detailed information of OS493_008856-T1 in Lophelia pertusa

Genomic Location: scaffold_21:681526...683226
NR annotation: KAJ7380399.1, mitochondrial mRNA catabolic process [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
Q3TIU4	2',5'-phosphodiesterase 12 OS=Mus musculus OX=10090 GN=Pde12 PE=1 SV=2
Q6AXQ5	2',5'-phosphodiesterase 12 OS=Rattus norvegicus OX=10116 GN=Pde12 PE=2 SV=1
Q08DF7	2',5'-phosphodiesterase 12 OS=Bos taurus OX=9913 GN=PDE12 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006892 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21171 all species →	PDE12-like_N	2',5'-phosphodiesterase 12-like, N-terminal domain	Domain	Interproscan
PF03372 all species →	Exo_endo_phos	Endonuclease/Exonuclease/phosphatase family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR048821 all species →	Domain	2',5'-phosphodiesterase 12-like, N-terminal domain	Interproscan
IPR005135 all species →	Domain	Endonuclease/exonuclease/phosphatase	Interproscan
IPR036691 all species →	Homologous_superfamily	Endonuclease/exonuclease/phosphatase superfamily	Interproscan
IPR050410 all species →	Family	CCR4/nocturin mRNA turnover and transcription	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12121 all species →	CARBON CATABOLITE REPRESSOR PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0000175 all species →	Molecular Function	3'-5'-RNA exonuclease activity	Interproscan
GO:0000288 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	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
K19612	PDE12; 2',5'-phosphodiesterase	EC:3.1.13.4 EC:3.1.4.-	Mitochondrial biogenesis	ko03029	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_008856-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

16.1Max TPM

4.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2.77	5.37
polyp at pH7 6	18	18	3.54	7.08
coral polyp · control treatment	16	16	6.30	12.42
coral polyp · oil and dispersant treatment	16	16	8.03	16.06
coral polyp · oil treatment	16	16	4.31	7.33
coral polyp · dispersant treatment	16	16	4.15	6.75
Polyp	10	9	2.18	6.64

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.37
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.75
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.49
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.27
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.97
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.96
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.89
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.79
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.75
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.75
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.73
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.64
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.43
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.26
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.11
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.91
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.78
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.03
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.08
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.14
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.43
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.90
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.70
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.55
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.45
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.29
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.28
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.11
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.73
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.35
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.27
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.15
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.25
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.42
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.07
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.93
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.40
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.14
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.12
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.47
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.03
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.26
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.88
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.47
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.21
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.94
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.43
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.02
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.06
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.25
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.18
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.50
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.47
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.45
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.76
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.72
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.31
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.02
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.16
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.08
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.49
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.46
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.24
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.33
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.03
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.97
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.74
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.72
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.72
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.44
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.09
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.09
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.98
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.65
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.53
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.78
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.47
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.16
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.28
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.75
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.56
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.22
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.85
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.65
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.56
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.36
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.17
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.16
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.83
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.92
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.62
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.41
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.64
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.24
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.63
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.48
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.45
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.29
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.23
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.08
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.74
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.