Gene detail

Detailed information of OS493_014568-T1 in Lophelia pertusa

Genomic Location: scaffold_41:1886232...1893605
NR annotation: KAJ7361921.1, hypothetical protein OS493_014568 [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
P14912	4-coumarate--CoA ligase 1 OS=Petroselinum crispum OX=4043 GN=4CL1 PE=2 SV=1
P14913	4-coumarate--CoA ligase 2 OS=Petroselinum crispum OX=4043 GN=4CL2 PE=2 SV=1
I3PB37	4-coumarate:CoA ligase 1 OS=Petunia hybrida OX=4102 GN=4CL1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000834 (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
IPR020845 all species →	Conserved_site	AMP-binding, conserved site	Interproscan
IPR000873 all species →	Domain	AMP-dependent synthetase/ligase domain	Interproscan
IPR025110 all species →	Domain	AMP-binding enzyme, C-terminal domain	Interproscan
IPR042099 all species →	Homologous_superfamily	ANL, N-terminal domain	Interproscan
IPR045851 all species →	Homologous_superfamily	AMP-binding enzyme, C-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24096 all species →	LONG-CHAIN-FATTY-ACID--COA LIGASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016405 all species →	Molecular Function	CoA-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
K01904	4CL; 4-coumarate--CoA ligase	EC:6.2.1.12	Phenylpropanoid biosynthesis	ko00940	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_014568-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

17.9Max TPM

5.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.11	12.55
polyp at pH7 6	18	18	6.31	10.32
coral polyp · control treatment	16	16	3.94	9.86
coral polyp · oil and dispersant treatment	16	15	1.67	3.32
coral polyp · oil treatment	16	16	3.19	7.91
coral polyp · dispersant treatment	16	16	5.40	17.91
Polyp	10	10	9.45	14.09

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.55
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.78
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.65
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.97
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.41
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.17
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.63
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.59
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.30
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.05
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.65
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.29
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.47
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.27
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.84
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.39
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.58
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.46
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.32
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.16
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.62
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.37
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.38
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.19
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.79
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.78
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.71
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.51
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.73
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.70
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.70
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.42
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.23
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.75
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.86
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.38
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.72
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.70
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.46
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.62
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.12
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.03
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.85
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.69
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.57
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.06
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.83
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.82
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.11
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.32
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.15
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.10
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.79
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.59
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.42
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.07
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.56
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.52
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.03
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.99
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.83
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.77
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.37
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.28
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.91
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.46
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.63
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.46
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.44
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.42
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.19
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.17
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.07
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.41
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.98
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.89
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.81
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.17
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.14
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.96
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.91
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.15
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.15
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.79
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.56
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.99
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.76
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.68
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.08
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.93
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.59
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.44
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.80
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.81
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.73
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	14.09
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	13.01
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	12.87
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.36
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.09
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.09
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.58
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.34
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.83
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.25

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.