Gene detail

Detailed information of OS493_028433-T1 in Lophelia pertusa

Genomic Location: scaffold_164:186175...192703
NR annotation: KAJ7383355.1, Hydroxymethylglutaryl-CoA synthase, cytoplasmic [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
P23228	Hydroxymethylglutaryl-CoA synthase, cytoplasmic OS=Gallus gallus OX=9031 GN=HMGCS1 PE=1 SV=1
P17425	Hydroxymethylglutaryl-CoA synthase, cytoplasmic OS=Rattus norvegicus OX=10116 GN=Hmgcs1 PE=1 SV=1
Q8JZK9	Hydroxymethylglutaryl-CoA synthase, cytoplasmic OS=Mus musculus OX=10090 GN=Hmgcs1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005551 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01154 all species →	HMG_CoA_synt_N	Hydroxymethylglutaryl-coenzyme A synthase N terminal	Domain	Interproscan
PF08540 all species →	HMG_CoA_synt_C	Hydroxymethylglutaryl-coenzyme A synthase C terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016039 all species →	Homologous_superfamily	Thiolase-like	Interproscan
IPR013528 all species →	Domain	Hydroxymethylglutaryl-coenzyme A synthase, N-terminal	Interproscan
IPR000590 all species →	Active_site	Hydroxymethylglutaryl-coenzyme A synthase, active site	Interproscan
IPR013746 all species →	Domain	Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain	Interproscan
IPR010122 all species →	Family	Hydroxymethylglutaryl-CoA synthase, eukaryotic	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43323 all species →	3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016746 all species →	Molecular Function	acyltransferase activity	Interproscan
GO:0004421 all species →	Molecular Function	hydroxymethylglutaryl-CoA synthase activity	Interproscan
GO:0006084 all species →	Biological Process	acetyl-CoA metabolic process	Interproscan
GO:0010142 all species →	Biological Process	farnesyl diphosphate biosynthetic process, mevalonate pathway	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
K01641	HMGCS; hydroxymethylglutaryl-CoA synthase	EC:2.3.3.10	PPAR signaling pathway	ko03320	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_028433-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

109TPM > 0

7Conditions

22.9Max TPM

5.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.56	5.34
polyp at pH7 6	18	18	4.59	8.86
coral polyp · control treatment	16	16	5.83	10.42
coral polyp · oil and dispersant treatment	16	16	8.49	15.04
coral polyp · oil treatment	16	16	5.10	9.03
coral polyp · dispersant treatment	16	16	9.64	22.88
Polyp	10	9	2.45	4.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.34
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.83
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.65
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.48
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.34
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.82
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.61
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.36
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.21
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.20
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.85
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.79
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.67
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.63
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.62
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.94
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.86
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.52
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.49
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.96
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.93
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.43
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.77
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.41
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.40
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.86
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.73
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.27
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.11
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.09
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.84
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.25
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.42
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.97
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.40
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.78
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.64
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.91
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.74
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.56
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.29
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.25
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.56
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.52
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.35
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.12
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.30
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.04
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.94
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.39
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.26
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.98
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.50
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.75
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.33
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.88
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.65
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.33
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.59
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.03
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.62
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.35
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.86
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.39
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.31
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.15
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.98
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.81
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.58
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.38
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.33
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.06
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.07
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.04
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.67
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.88
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.13
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.64
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.83
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.47
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.59
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.93
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.93
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.35
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.13
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.38
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.94
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.57
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.86
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.05
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.48
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.18
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.15
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.34
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.69
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.58
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.33
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.06
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.02
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.15
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.