Gene detail

Detailed information of OS493_034455-T1 in Lophelia pertusa

Genomic Location: scaffold_291:184486...196902
NR annotation: KAJ7376465.1, Acyl-coenzyme A synthetase acsm4, mitochondrial-like [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
P0C7M7	Acyl-coenzyme A synthetase ACSM4, mitochondrial OS=Homo sapiens OX=9606 GN=ACSM4 PE=1 SV=1
Q3UNX5	Acyl-coenzyme A synthetase ACSM3, mitochondrial OS=Mus musculus OX=10090 GN=Acsm3 PE=1 SV=2
Q53FZ2	Acyl-coenzyme A synthetase ACSM3, mitochondrial OS=Homo sapiens OX=9606 GN=ACSM3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001394 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00501 all species →	AMP-binding	AMP-binding enzyme	Family	Interproscan
PF13193 all species →	AMP-binding_C	AMP-binding enzyme C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR042099 all species →	Homologous_superfamily	ANL, N-terminal domain	Interproscan
IPR051087 all species →	Family	Mitochondrial Acyl-CoA Synthetase Medium-Chain	Interproscan
IPR000873 all species →	Domain	AMP-dependent synthetase/ligase domain	Interproscan
IPR025110 all species →	Domain	AMP-binding enzyme, C-terminal domain	Interproscan
IPR045851 all species →	Homologous_superfamily	AMP-binding enzyme, C-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43605 all species →	ACYL-COENZYME A SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004321 all species →	Molecular Function	fatty-acyl-CoA synthase activity	Interproscan
GO:0005759 all species →	Cellular Component	mitochondrial matrix	Interproscan
GO:0006633 all species →	Biological Process	fatty acid biosynthetic process	Interproscan
GO:0006637 all species →	Biological Process	acyl-CoA metabolic process	Interproscan
GO:0015645 all species →	Molecular Function	fatty acid ligase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K01896	ACSM; medium-chain acyl-CoA synthetase	EC:6.2.1.2	Lipid biosynthesis proteins	ko01004	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_034455-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

28.8Max TPM

12.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	18.31	26.00
polyp at pH7 6	18	18	16.68	27.67
coral polyp · control treatment	16	16	11.57	28.80
coral polyp · oil and dispersant treatment	16	16	10.18	22.47
coral polyp · oil treatment	16	16	12.91	27.06
coral polyp · dispersant treatment	16	16	8.27	22.63
Polyp	10	10	4.45	7.41

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	-	26.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.61
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.23
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.22
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.95
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.38
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.84
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.47
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.01
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.22
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.62
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.88
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.15
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.07
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.37
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.37
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.62
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.63
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.67
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.28
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.51
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.47
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.08
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.70
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.32
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.33
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.07
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.45
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.21
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.66
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.22
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.31
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.86
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.84
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.80
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.12
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.09
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.54
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.37
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.85
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.32
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.26
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.40
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.24
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.80
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.01
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.47
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.16
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.80
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.67
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.93
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.22
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.13
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.20
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.18
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.77
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.58
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.43
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.01
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.54
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.98
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.74
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.06
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.19
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.87
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.12
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.68
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.44
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.08
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.69
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.07
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.32
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.40
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.74
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.54
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.76
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.77
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.61
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.78
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.20
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.44
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.86
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.49
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.39
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.27
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.20
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.85
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.73
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.71
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.41
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.79
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.17
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.92
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.72
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.04
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.48
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.26
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.99
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.78

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.