Gene detail

Detailed information of OS493_026402-T1 in Lophelia pertusa

Genomic Location: scaffold_135:879206...887404
NR annotation: KAJ7377834.1, hypothetical protein OS493_026402 [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
Q5E9B3	Geranylgeranyl transferase type-2 subunit beta OS=Bos taurus OX=9913 GN=RABGGTB PE=2 SV=1
P53611	Geranylgeranyl transferase type-2 subunit beta OS=Homo sapiens OX=9606 GN=RABGGTB PE=1 SV=2
Q08603	Geranylgeranyl transferase type-2 subunit beta OS=Rattus norvegicus OX=10116 GN=Rabggtb PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006218 (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
IPR008930 all species →	Homologous_superfamily	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Interproscan
IPR026873 all species →	Family	Geranylgeranyl transferase type-2 subunit beta	Interproscan
IPR001330 all species →	Repeat	PFTB repeat	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:0004663 all species →	Molecular Function	Rab geranylgeranyltransferase activity	Interproscan
GO:0018344 all species →	Biological Process	protein geranylgeranylation	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0005968 all species →	Cellular Component	Rab-protein geranylgeranyltransferase complex	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
K05956	RABGGTB; geranylgeranyl transferase type-2 subunit beta	EC:2.5.1.60	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_026402-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

92.1Max TPM

37.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	45.62	82.53
polyp at pH7 6	18	18	46.90	91.69
coral polyp · control treatment	16	16	40.33	67.85
coral polyp · oil and dispersant treatment	16	16	29.54	54.96
coral polyp · oil treatment	16	16	38.83	63.53
coral polyp · dispersant treatment	16	16	18.16	35.64
Polyp	10	10	41.07	92.07

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	82.53
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	74.46
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.10
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.25
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.99
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.22
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.39
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.26
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.08
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.90
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.01
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.84
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.37
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.25
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.16
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.94
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.99
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.50
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	91.69
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	77.10
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.59
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.09
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.17
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.32
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.25
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.96
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.88
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.62
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.11
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.37
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.91
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.83
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.23
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.43
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.43
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.85
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.57
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.38
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.64
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.56
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.80
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.60
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.24
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.24
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.99
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.36
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.09
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.65
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.99
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.07
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.96
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.00
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.16
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.35
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.88
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.11
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.84
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.23
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.76
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.54
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.11
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.51
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.95
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.85
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.63
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.73
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.53
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.45
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.37
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.16
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.56
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.06
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.51
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.10
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.95
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.41
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.29
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.27
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.14
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.11
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.94
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.64
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.72
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.55
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.43
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.02
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.14
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.82
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.74
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.23
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.29
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.07
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.77
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.53
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.33
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.94
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.31
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	92.07
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	45.93
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	43.51
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	42.23
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	38.46
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	38.20
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	33.59
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	33.17
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	23.29
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	20.27

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.