Gene detail

Detailed information of OS493_006833-T1 in Lophelia pertusa

Genomic Location: scaffold_14:2707244...2708157
NR annotation: KAJ7386804.1, hypothetical protein OS493_006833 [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
P49355	Protein farnesyltransferase subunit beta OS=Bos taurus OX=9913 GN=FNTB PE=2 SV=1
P49356	Protein farnesyltransferase subunit beta OS=Homo sapiens OX=9606 GN=FNTB PE=1 SV=1
Q02293	Protein farnesyltransferase subunit beta OS=Rattus norvegicus OX=10116 GN=Fntb PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006763 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00432 all species →	Prenyltrans	Prenyltransferase and squalene oxidase repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045089 all species →	Family	Prenyltransferase subunit beta	Interproscan
IPR008930 all species →	Homologous_superfamily	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Interproscan
IPR001330 all species →	Repeat	PFTB repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11774 all species →	GERANYLGERANYL TRANSFERASE TYPE BETA SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004660 all species →	Molecular Function	protein farnesyltransferase activity	Interproscan
GO:0005965 all species →	Cellular Component	protein farnesyltransferase complex	Interproscan
GO:0008318 all species →	Molecular Function	protein prenyltransferase activity	Interproscan
GO:0018342 all species →	Biological Process	protein prenylation	Interproscan
GO:0018343 all species →	Biological Process	protein farnesylation	Interproscan
GO:0003824 all species →	Molecular Function	catalytic 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

No KEGG orthology assignment for OS493_006833-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_006833-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

107TPM > 0

7Conditions

69.0Max TPM

10.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.94	9.05
polyp at pH7 6	18	16	5.50	11.15
coral polyp · control treatment	16	16	11.47	30.18
coral polyp · oil and dispersant treatment	16	16	14.39	35.78
coral polyp · oil treatment	16	16	7.66	12.42
coral polyp · dispersant treatment	16	16	22.81	69.03
Polyp	10	9	3.16	4.71

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	-	9.05
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.79
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.52
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.31
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.99
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.67
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.28
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.20
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.00
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.93
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.23
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.82
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.37
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.33
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.66
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.50
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.15
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.42
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.13
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.73
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.64
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.08
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.51
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.84
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.24
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.80
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.48
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.64
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.16
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	30.18
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.79
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.42
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.22
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.12
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.80
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.71
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.80
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.80
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.55
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.12
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.94
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.78
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.71
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.88
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.78
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.60
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.75
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.27
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.09
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.74
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.25
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.81
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.39
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.13
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.31
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.26
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.28
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.41
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.40
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.78
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.42
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.64
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.30
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.12
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.99
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.84
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.72
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.28
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.96
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.29
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.72
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.27
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.79
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.48
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.03
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.37
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.86
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.42
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.94
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.69
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.36
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.08
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.91
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.46
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.65
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.67
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.91
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.71
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.48
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.47
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.42
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.88
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.06
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.38
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.13
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.03
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.