Gene detail

Detailed information of OS493_027909-T1 in Lophelia pertusa

Genomic Location: scaffold_155:626626...632313
NR annotation: KAJ7355120.1, protein phosphatase 4, regulatory subunit 2 [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
Q9W2U4	Serine/threonine-protein phosphatase 4 regulatory subunit 2 OS=Drosophila melanogaster OX=7227 GN=PPP4R2r PE=1 SV=2
A1L1M4	Serine/threonine-protein phosphatase 4 regulatory subunit 2-B OS=Danio rerio OX=7955 GN=ppp4r2b PE=1 SV=2
Q28IG6	Serine/threonine-protein phosphatase 4 regulatory subunit 2 OS=Xenopus tropicalis OX=8364 GN=ppp4r2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006190 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09184 all species →	PPP4R2	PPP4R2	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015267 all species →	Family	Protein phosphatase 4 core regulatory subunit R2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16487 all species →	PPP4R2-RELATED PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0019888 all species →	Molecular Function	protein phosphatase regulator activity	Interproscan
GO:0030289 all species →	Cellular Component	protein phosphatase 4 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K15425	PPP4R2; serine/threonine-protein phosphatase 4 regulatory subunit 2	-	DNA repair and recombination proteins	ko03400	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_027909-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

80.6Max TPM

24.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.30	27.86
polyp at pH7 6	18	18	18.73	28.12
coral polyp · control treatment	16	16	29.91	80.60
coral polyp · oil and dispersant treatment	16	16	36.31	61.00
coral polyp · oil treatment	16	16	24.06	32.36
coral polyp · dispersant treatment	16	16	28.59	40.96
Polyp	10	10	13.89	20.01

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	-	27.86
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.76
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.12
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.16
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.87
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.20
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.06
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.65
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.23
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.10
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.21
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.18
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.63
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.32
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.97
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.34
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.71
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.12
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.20
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.19
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.43
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.46
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.46
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.16
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.47
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.14
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.39
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.32
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.78
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.86
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.12
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.42
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.60
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.04
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.06
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.14
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.52
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.86
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.40
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.52
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.58
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.62
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.44
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.22
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.64
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.76
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.67
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.26
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.73
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.21
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.25
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.00
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.09
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.57
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.13
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.75
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.37
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.10
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.89
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.36
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.09
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.76
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.74
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.63
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.17
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.75
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.63
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.67
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.07
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.55
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.31
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.24
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.26
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.42
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.34
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.96
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.24
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.96
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.21
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.83
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.55
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.81
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.86
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.68
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.32
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.63
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.54
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.50
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.68
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.89
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.70
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	20.01
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.18
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.63
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.40
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	13.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	12.81
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.51
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.96

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.