Gene detail

Detailed information of OS493_039704-T1 in Lophelia pertusa

Genomic Location: scaffold_1389:1895...13003
NR annotation: KAJ7375668.1, hypothetical protein OS493_039704, partial [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
P08836	Farnesyl pyrophosphate synthase OS=Gallus gallus OX=9031 GN=FDPS PE=1 SV=2
Q920E5	Farnesyl pyrophosphate synthase OS=Mus musculus OX=10090 GN=Fdps PE=1 SV=1
P05369	Farnesyl pyrophosphate synthase OS=Rattus norvegicus OX=10116 GN=Fdps PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004118 (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
IPR000092 all species →	Family	Polyprenyl synthetase	Interproscan
IPR008949 all species →	Homologous_superfamily	Isoprenoid synthase domain superfamily	Interproscan
IPR039702 all species →	Family	Farnesyl pyrophosphate synthase-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11525 all species →	FARNESYL-PYROPHOSPHATE SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008299 all species →	Biological Process	isoprenoid biosynthetic process	Interproscan
GO:0004161 all species →	Molecular Function	dimethylallyltranstransferase activity	Interproscan
GO:0004337 all species →	Molecular Function	geranyltranstransferase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0016765 all species →	Molecular Function	transferase activity, transferring alkyl or aryl (other than methyl) groups	Interproscan
GO:0045337 all species →	Biological Process	farnesyl diphosphate 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

No KEGG orthology assignment for OS493_039704-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_039704-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

87TPM > 0

7Conditions

7.6Max TPM

2.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	10	1.67	5.23
polyp at pH7 6	18	9	1.21	4.71
coral polyp · control treatment	16	16	3.51	7.28
coral polyp · oil and dispersant treatment	16	14	2.19	3.96
coral polyp · oil treatment	16	16	3.08	5.45
coral polyp · dispersant treatment	16	14	2.11	5.70
Polyp	10	8	2.77	7.61

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.23
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.90
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.88
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.71
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.94
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.36
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.18
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.45
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.44
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359510	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
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.71
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.10
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.29
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.24
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.09
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.91
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.81
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.65
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.99
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359515	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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.28
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.46
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.08
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.71
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.90
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.38
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.15
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.97
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.91
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.86
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.64
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.49
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.07
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.33
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.16
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.96
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.31
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.14
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.54
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.14
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.97
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.74
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.73
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.70
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.45
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.59
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.66
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.21
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.20
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.12
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.08
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.90
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.86
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.63
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.45
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.35
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.42
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.64
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.87
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.51
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.46
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.09
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.66
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.46
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.36
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.24
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.10
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.61
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.23
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.12
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.03
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.18
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.16
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.95
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.