Gene detail

Detailed information of OS493_006319-T1 in Lophelia pertusa

Genomic Location: scaffold_13:1979200...1984331
NR annotation: KAJ7393348.1, Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta [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
Q95142	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta OS=Bos taurus OX=9913 GN=PDE6D PE=1 SV=1
Q9XT54	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta OS=Canis lupus familiaris OX=9615 GN=PDE6D PE=2 SV=1
O43924	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta OS=Homo sapiens OX=9606 GN=PDE6D PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007900 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05351 all species →	GMP_PDE_delta	GMP-PDE, delta subunit	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017287 all species →	Family	Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit	Interproscan
IPR037036 all species →	Homologous_superfamily	GMP phosphodiesterase, delta subunit superfamily	Interproscan
IPR014756 all species →	Homologous_superfamily	Immunoglobulin E-set	Interproscan
IPR008015 all species →	Domain	GMP phosphodiesterase, delta subunit	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12976 all species →	RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE DELTA-SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0050953 all species →	Biological Process	sensory perception of light stimulus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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
K13758	PDE6D; retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	-	Membrane trafficking	ko04131	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_006319-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

144.5Max TPM

57.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	40.44	56.55
polyp at pH7 6	18	18	42.76	70.62
coral polyp · control treatment	16	16	76.66	144.50
coral polyp · oil and dispersant treatment	16	16	72.43	107.59
coral polyp · oil treatment	16	16	66.02	103.70
coral polyp · dispersant treatment	16	16	62.39	89.50
Polyp	10	10	36.95	67.83

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.55
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.64
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.58
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.88
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.59
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.33
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.20
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.05
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.77
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.68
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.65
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.58
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.49
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.24
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.40
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.84
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.80
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.59
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.62
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.22
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.25
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.11
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.92
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.55
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.46
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.28
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.83
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.69
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.18
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.74
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.76
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.16
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.66
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.76
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.16
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	144.50
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	119.03
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.32
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.95
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.97
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.34
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.24
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.33
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.05
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.77
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.20
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.06
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.01
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.85
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.85
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.10
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.59
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	99.07
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	93.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.99
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.29
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.19
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.80
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.03
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.96
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.03
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.62
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.58
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.44
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.93
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.70
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.40
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	93.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.62
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.14
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.49
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.38
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.99
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.63
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.77
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.34
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.72
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.46
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.15
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.45
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	89.50
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	89.18
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.92
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.17
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.41
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.33
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.76
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.07
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.40
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.04
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.17
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.64
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.56
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.29
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.88
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.86
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	67.83
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	56.98
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	55.19
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	54.42
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	37.08
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	29.77
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	24.82
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.32
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.58
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	13.50

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.