Gene detail

Detailed information of OS493_019580-T1 in Lophelia pertusa

Genomic Location: scaffold_69:68816...114567
NR annotation: KAJ7378889.1, Geranylgeranyl transferase type-1 subunit beta [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
Q5EAD5	Geranylgeranyl transferase type-1 subunit beta OS=Bos taurus OX=9913 GN=PGGT1B PE=2 SV=1
P53610	Geranylgeranyl transferase type-1 subunit beta OS=Rattus norvegicus OX=10116 GN=Pggt1b PE=1 SV=1
P53609	Geranylgeranyl transferase type-1 subunit beta OS=Homo sapiens OX=9606 GN=PGGT1B PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005070 (this species only)

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
IPR001330 all species →	Repeat	PFTB repeat	Interproscan
IPR008930 all species →	Homologous_superfamily	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Interproscan
IPR041960 all species →	Family	Geranylgeranyl transferase type-1 subunit beta	Interproscan
IPR045089 all species →	Family	Prenyltransferase subunit beta	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0004661 all species →	Molecular Function	protein geranylgeranyltransferase activity	Interproscan
GO:0005953 all species →	Cellular Component	CAAX-protein geranylgeranyltransferase complex	Interproscan
GO:0018344 all species →	Biological Process	protein geranylgeranylation	Interproscan
GO:0004662 all species →	Molecular Function	CAAX-protein geranylgeranyltransferase activity	Interproscan
GO:0008318 all species →	Molecular Function	protein prenyltransferase activity	Interproscan
GO:0018342 all species →	Biological Process	protein prenylation	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
K11713	PGTB1; geranylgeranyl transferase type-1 subunit beta	EC:2.5.1.59	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_019580-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

22.8Max TPM

10.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.76	12.15
polyp at pH7 6	18	18	9.35	14.03
coral polyp · control treatment	16	16	12.47	16.47
coral polyp · oil and dispersant treatment	16	16	11.15	14.85
coral polyp · oil treatment	16	16	10.62	15.55
coral polyp · dispersant treatment	16	16	13.89	22.83
Polyp	10	10	7.52	11.38

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	-	12.15
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.95
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.94
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.45
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.05
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.86
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.36
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.17
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.91
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.45
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.26
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.91
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.81
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.99
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.60
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.71
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.78
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.03
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.14
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.40
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.44
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.29
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.25
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.04
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.77
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.68
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.10
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.03
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.03
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.96
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.88
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.48
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.69
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.47
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.15
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.98
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.67
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.58
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.39
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.06
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.20
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.12
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.68
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.33
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.39
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.67
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.66
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.40
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.75
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.85
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.69
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.85
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.83
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.22
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.70
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.95
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.43
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.39
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.05
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.98
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.74
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.68
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.47
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.41
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.15
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.55
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.89
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.48
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.86
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.75
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.50
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.36
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.12
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.86
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.36
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.01
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.21
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.34
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.63
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.20
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.83
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.97
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.56
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.92
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.94
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.90
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.74
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.43
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.26
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.83
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.98
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.42
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.16
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.33
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.27
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.74
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.38
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.30
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.50
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.20
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.15
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.07
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.37
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.96
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.99

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.