Gene detail

Detailed information of OS493_012520-T1 in Lophelia pertusa

Genomic Location: scaffold_33:127382...143456
NR annotation: KAJ7379774.1, hypothetical protein OS493_012520 [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
Q9LU36	4-coumarate--CoA ligase 4 OS=Arabidopsis thaliana OX=3702 GN=4CL4 PE=1 SV=1
A0A6B9HER0	Piperic acid--CoA ligase OS=Piper nigrum OX=13216 PE=1 SV=1
Q7XXL2	4-coumarate--CoA ligase-like 9 OS=Oryza sativa subsp. japonica OX=39947 GN=4CLL9 PE=1 SV=2

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

InterPro

InterPro term	Type	Description	Source
IPR020845 all species →	Conserved_site	AMP-binding, conserved site	Interproscan
IPR042099 all species →	Homologous_superfamily	ANL, N-terminal domain	Interproscan
IPR000873 all species →	Domain	AMP-dependent synthetase/ligase domain	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
K04096	smf; DNA processing protein	-	Replication and repair	-	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_012520-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

59.8Max TPM

15.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.12	39.50
polyp at pH7 6	18	17	14.00	20.50
coral polyp · control treatment	16	16	18.52	33.87
coral polyp · oil and dispersant treatment	16	16	10.90	22.74
coral polyp · oil treatment	16	16	15.39	40.84
coral polyp · dispersant treatment	16	16	12.00	26.73
Polyp	10	10	19.40	59.84

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.17
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.97
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.59
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.16
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.62
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.32
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.81
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.46
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.61
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.64
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.25
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.19
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.36
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.10
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.31
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.65
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.41
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.34
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.51
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.03
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.75
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.66
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.04
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.82
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.15
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.14
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.20
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.59
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.63
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.87
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.29
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.68
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.79
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.53
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.41
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.46
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.76
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.57
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.27
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.18
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.77
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.30
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.80
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.74
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.30
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.30
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.56
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.34
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.21
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.12
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.97
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.76
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.69
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.61
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.81
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.19
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.79
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.32
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.99
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.74
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.11
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.89
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.70
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.28
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.22
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.34
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.14
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.60
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.09
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.92
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.73
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.75
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.06
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.95
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.50
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.36
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.75
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.36
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.84
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.06
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.36
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.67
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.32
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.84
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	59.84
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	45.07
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	20.07
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	17.42
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.05
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.11
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	10.23
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.46
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.54

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.