Gene detail

Detailed information of OS493_013268-T1 in Lophelia pertusa

Genomic Location: scaffold_35:2112435...2118549
NR annotation: KAJ7362174.1, Geranylgeranyl pyrophosphate synthase [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
P56966	Geranylgeranyl pyrophosphate synthase OS=Bos taurus OX=9913 GN=GGPS1 PE=1 SV=2
O95749	Geranylgeranyl pyrophosphate synthase OS=Homo sapiens OX=9606 GN=GGPS1 PE=1 SV=1
Q9WTN0	Geranylgeranyl pyrophosphate synthase OS=Mus musculus OX=10090 GN=Ggps1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009653 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00348 all species →	polyprenyl_synt	Polyprenyl synthetase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008949 all species →	Homologous_superfamily	Isoprenoid synthase domain superfamily	Interproscan
IPR000092 all species →	Family	Polyprenyl synthetase	Interproscan
IPR033749 all species →	Conserved_site	Polyprenyl synthetase, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12001 all species →	GERANYLGERANYL PYROPHOSPHATE SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004659 all species →	Molecular Function	prenyltransferase activity	Interproscan
GO:0008299 all species →	Biological Process	isoprenoid biosynthetic process	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
K00804	GGPS1; geranylgeranyl diphosphate synthase, type III	EC:2.5.1.1 EC:2.5.1.10 EC:2.5.1.29	Prenyltransferases	ko01006	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_013268-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

103TPM > 0

7Conditions

17.9Max TPM

8.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	8.19	14.18
polyp at pH7 6	18	15	8.93	15.88
coral polyp · control treatment	16	16	10.34	16.29
coral polyp · oil and dispersant treatment	16	16	8.84	14.64
coral polyp · oil treatment	16	16	10.84	16.20
coral polyp · dispersant treatment	16	15	5.75	11.41
Polyp	10	9	8.67	17.86

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.18
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.46
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.53
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.41
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.06
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.26
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.14
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.04
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.86
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.83
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.17
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.96
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.71
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.03
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.16
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.88
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.33
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.45
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.18
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.06
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.71
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.62
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.20
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.80
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.75
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.49
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.84
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.34
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.12
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.02
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.29
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.36
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.22
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.18
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.11
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.80
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.54
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.46
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.39
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.75
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.27
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.62
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.33
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.11
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.64
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.26
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.75
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.63
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.27
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.72
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.30
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.50
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.37
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.22
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.90
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.79
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.35
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.10
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.44
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.18
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.20
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.12
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.01
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.07
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.86
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.91
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.07
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.63
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.30
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.56
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.19
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.78
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.45
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.35
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.41
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.41
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.63
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.62
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.18
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.25
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.97
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.24
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.04
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.31
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.80
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.93
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.52
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.57
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	17.86
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.72
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	13.25
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.63
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.80
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.60
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.75
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.08
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.