Gene detail

Detailed information of OS493_039478-T1 in Lophelia pertusa

Genomic Location: scaffold_1189:9228...16591
NR annotation: KAJ7388165.1, Acyl-CoA synthetase short-chain member 3, mitochondrial [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
Q14DH7	Acyl-CoA synthetase short-chain family member 3, mitochondrial OS=Mus musculus OX=10090 GN=Acss3 PE=1 SV=2
A0A0G2K047	Acyl-CoA synthetase short-chain family member 3, mitochondrial OS=Rattus norvegicus OX=10116 GN=Acss3 PE=1 SV=1
A7MB45	Acyl-CoA synthetase short-chain family member 3, mitochondrial OS=Bos taurus OX=9913 GN=ACSS3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000999 (this species only)

Pfam domain

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

InterPro

InterPro term	Type	Description	Source
IPR025110 all species →	Domain	AMP-binding enzyme, C-terminal domain	Interproscan
IPR045851 all species →	Homologous_superfamily	AMP-binding enzyme, C-terminal domain superfamily	Interproscan
IPR000873 all species →	Domain	AMP-dependent synthetase/ligase domain	Interproscan
IPR042099 all species →	Homologous_superfamily	ANL, N-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43347 all species →	ACYL-COA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005759 all species →	Cellular Component	mitochondrial matrix	Interproscan
GO:0050218 all species →	Molecular Function	propionate-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

No KEGG orthology assignment for OS493_039478-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_039478-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

130.7Max TPM

26.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.67	36.35
polyp at pH7 6	18	18	23.17	41.81
coral polyp · control treatment	16	16	30.01	61.99
coral polyp · oil and dispersant treatment	16	16	36.65	130.73
coral polyp · oil treatment	16	16	33.51	71.83
coral polyp · dispersant treatment	16	16	22.33	34.07
Polyp	10	10	7.11	17.76

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.35
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.28
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.31
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.16
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.06
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.21
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.83
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.55
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.22
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.63
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.66
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.53
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.22
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.42
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.47
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.91
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.39
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.93
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.35
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.92
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.69
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.24
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.55
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.22
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.75
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.35
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.90
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.44
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.12
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.81
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.24
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.07
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.55
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.37
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.99
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.85
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.78
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.47
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.08
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.56
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.37
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.98
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.96
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.08
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.67
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.42
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.79
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.86
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.88
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	130.73
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.94
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.03
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.68
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.56
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.52
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.82
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.90
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.93
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.98
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.43
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.05
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.05
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.83
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.63
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.49
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.56
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.57
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.82
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.96
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.92
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.08
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.06
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.14
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.07
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.92
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.66
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.35
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.48
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.42
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.34
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.94
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.26
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.79
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.12
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.76
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.59
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.96
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.09
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.52
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	17.76
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	13.65
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.09
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	8.97
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.30
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.24
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.30
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.61

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.