Gene detail

Detailed information of OS493_015473-T1 in Lophelia pertusa

Genomic Location: scaffold_46:2203078...2204734
NR annotation: KAJ7373003.1, Cysteine protease atg4c [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
Q68EP9	Cysteine protease ATG4C OS=Xenopus tropicalis OX=8364 GN=atg4c PE=2 SV=1
Q5XH30	Cysteine protease ATG4C OS=Xenopus laevis OX=8355 GN=atg4c PE=2 SV=1
Q811C2	Cysteine protease ATG4C OS=Mus musculus OX=10090 GN=Atg4c PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001754 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03416 all species →	Peptidase_C54	Peptidase family C54	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005078 all species →	Family	Peptidase C54	Interproscan
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan
IPR046792 all species →	Domain	Peptidase C54, catalytic domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22624 all species →	CYSTEINE PROTEASE ATG4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008234 all species →	Molecular Function	cysteine-type peptidase activity	Interproscan
GO:0019786 all species →	Molecular Function	protein-phosphatidylethanolamide deconjugating 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_015473-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_015473-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

107TPM > 0

7Conditions

31.6Max TPM

11.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.72	20.13
polyp at pH7 6	18	16	12.27	19.47
coral polyp · control treatment	16	16	14.98	31.60
coral polyp · oil and dispersant treatment	16	16	9.14	21.63
coral polyp · oil treatment	16	16	13.87	23.53
coral polyp · dispersant treatment	16	16	7.80	13.89
Polyp	10	9	8.82	18.80

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.13
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.73
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.24
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.70
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.90
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.43
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.35
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.18
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.41
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.24
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.07
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.99
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.38
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.16
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.56
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.49
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.47
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.35
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.18
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.48
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.72
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.44
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.21
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.17
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.45
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.35
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.88
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.51
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.55
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.53
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.15
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.60
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.74
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.17
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.82
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.36
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.20
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.41
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.75
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.30
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.82
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.90
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.66
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.91
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.28
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.04
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.63
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.28
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.78
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.92
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.87
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.48
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.30
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.90
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.89
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.69
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.66
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.14
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.71
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.93
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.45
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.53
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.94
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.52
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.94
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.22
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.87
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.46
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.06
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.36
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.77
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.17
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.12
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.11
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.95
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.25
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.89
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.28
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.93
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.88
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.87
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.90
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.39
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.68
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.53
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.73
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.58
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.14
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.85
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.76
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.81
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	18.80
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.99
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.61
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.56
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.35
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.17
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.22
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.99
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.51
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.