Gene detail

Detailed information of OS493_038031-T1 in Lophelia pertusa

Genomic Location: scaffold_494:82708...98039
NR annotation: KAJ7381955.1, SMEK 2, suppressor of mek1 (Dictyostelium) [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
Q6P2K6	Serine/threonine-protein phosphatase 4 regulatory subunit 3A OS=Mus musculus OX=10090 GN=Ppp4r3a PE=1 SV=1
Q6IN85	Serine/threonine-protein phosphatase 4 regulatory subunit 3A OS=Homo sapiens OX=9606 GN=PPP4R3A PE=1 SV=1
Q4S6U8	Serine/threonine-protein phosphatase 4 regulatory subunit 3 OS=Tetraodon nigroviridis OX=99883 GN=smek1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005494 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04802 all species →	PP4R3	Phosphatase 4 regulatory subunit 3	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006887 all species →	Domain	Serine/threonine-protein phosphatase 4 regulatory subunit 3-like, central domain	Interproscan
IPR051137 all species →	Family	Serine/threonine-protein phosphatase 4 regulatory subunit 3	Interproscan
IPR011993 all species →	Homologous_superfamily	PH-like domain superfamily	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23318 all species →	ATP SYNTHASE GAMMA-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005654 all species →	Cellular Component	nucleoplasm	Interproscan
GO:0006470 all species →	Biological Process	protein dephosphorylation	Interproscan
GO:0006974 all species →	Biological Process	DNA damage response	Interproscan
GO:0030289 all species →	Cellular Component	protein phosphatase 4 complex	Interproscan
GO:0072542 all species →	Molecular Function	protein phosphatase activator activity	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
K17491	SMEK, PPP4R3; protein phosphatase 4 regulatory subunit 3	-	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_038031-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

100.2Max TPM

43.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	38.97	67.36
polyp at pH7 6	18	18	38.47	51.98
coral polyp · control treatment	16	16	51.10	100.18
coral polyp · oil and dispersant treatment	16	16	54.98	86.65
coral polyp · oil treatment	16	16	41.56	67.23
coral polyp · dispersant treatment	16	16	45.06	69.23
Polyp	10	10	25.57	44.85

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	67.36
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.31
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.43
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.62
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.57
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.15
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.43
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.50
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.34
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.68
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.56
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.29
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.26
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.83
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.56
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.58
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.86
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.98
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.50
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.43
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.62
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.41
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.57
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.20
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.49
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.22
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.71
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.64
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.93
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.55
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.36
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.22
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.47
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	100.18
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.27
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.57
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.02
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.75
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.65
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.83
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.93
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.62
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.64
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.30
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.51
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.58
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.16
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.25
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.33
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.65
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.80
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.29
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.10
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.24
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.39
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.27
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.64
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.61
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.19
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.06
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.42
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.86
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.40
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	67.23
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.21
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.51
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.54
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.29
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.67
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.09
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.48
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.03
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.29
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.68
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.46
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.84
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.23
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.26
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.35
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.56
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.05
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.99
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.61
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.54
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.38
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.15
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.18
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.75
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.37
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.20
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.03
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.30
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	44.85
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	42.26
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	34.55
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	29.14
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	27.50
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	25.36
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	18.06
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.08
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	12.12
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.77

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.