Gene detail

Detailed information of OS493_010520-T1 in Lophelia pertusa

Genomic Location: scaffold_25:2676393...2681294
NR annotation: KAJ7392859.1, E2-like enzyme [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
Q6GQE7	Ubiquitin-like-conjugating enzyme ATG3 OS=Xenopus laevis OX=8355 GN=atg3 PE=2 SV=1
Q9CPX6	Ubiquitin-like-conjugating enzyme ATG3 OS=Mus musculus OX=10090 GN=Atg3 PE=1 SV=1
Q6AZ50	Ubiquitin-like-conjugating enzyme ATG3 OS=Rattus norvegicus OX=10116 GN=Atg3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006563 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03987 all species →	Autophagy_act_C	Autophagocytosis associated protein, active-site domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR046962 all species →	Family	Autophagy-related protein 3	Interproscan
IPR007135 all species →	Family	Ubiquitin-like-conjugating enzyme Atg3/Atg10	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12866 all species →	UBIQUITIN-LIKE-CONJUGATING ENZYME ATG3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000045 all species →	Biological Process	autophagosome assembly	Interproscan
GO:0000407 all species →	Cellular Component	phagophore assembly site	Interproscan
GO:0000422 all species →	Biological Process	autophagy of mitochondrion	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0019776 all species →	Molecular Function	Atg8-family ligase activity	Interproscan
GO:0044804 all species →	Biological Process	nucleophagy	Interproscan
GO:0019787 all species →	Molecular Function	ubiquitin-like protein transferase 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
K08343	ATG3; ubiquitin-like-conjugating enzyme ATG3	-	Mitochondrial biogenesis	ko03029	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_010520-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

42.7Max TPM

21.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.34	26.29
polyp at pH7 6	18	18	21.05	31.24
coral polyp · control treatment	16	16	26.84	42.66
coral polyp · oil and dispersant treatment	16	16	22.07	36.48
coral polyp · oil treatment	16	16	23.49	36.82
coral polyp · dispersant treatment	16	16	22.43	37.34
Polyp	10	9	10.56	18.34

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.29
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.47
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.25
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.08
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.60
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.12
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.82
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.59
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.77
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.57
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.45
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.55
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.06
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.32
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.06
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.89
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.50
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.24
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.11
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.14
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.99
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.06
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.98
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.78
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.68
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.02
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.90
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.60
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.43
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.13
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.29
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.56
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.73
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.66
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.28
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.06
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.03
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.84
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.38
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.52
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.51
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.24
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.01
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.63
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.70
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.18
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.15
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.63
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.48
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.84
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.20
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.43
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.05
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.28
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.18
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.89
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.99
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.32
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.33
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.77
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.59
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.66
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.11
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.02
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.82
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.87
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.92
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.75
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.40
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.16
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.50
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.83
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.21
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.11
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.38
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.16
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.02
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.32
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.34
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.21
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.32
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.26
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.66
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.69
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.10
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.34
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.95
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.44
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.09
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.81
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.57
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.82
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.11
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.22
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	18.34
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.72
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.66
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.59
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.64
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.27
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.43
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.87
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.