Gene detail

Detailed information of OS493_019760-T1 in Lophelia pertusa

Genomic Location: scaffold_70:762287...773607
NR annotation: KAJ7372316.1, Ubiquitin carboxyl-terminal hydrolase 20 [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
Q5R5Z6	Ubiquitin carboxyl-terminal hydrolase 20 OS=Pongo abelii OX=9601 GN=USP20 PE=2 SV=1
Q9Y2K6	Ubiquitin carboxyl-terminal hydrolase 20 OS=Homo sapiens OX=9606 GN=USP20 PE=1 SV=2
A7Z056	Ubiquitin carboxyl-terminal hydrolase 20 OS=Bos taurus OX=9913 GN=USP20 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003770 (this species only)
Ubiquitin family	DUB\|USP\|USP · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06337 all species →	DUSP	DUSP domain	Domain	Interproscan
PF00443 all species →	UCH	Ubiquitin carboxyl-terminal hydrolase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006615 all species →	Domain	Peptidase C19, ubiquitin-specific peptidase, DUSP domain	Interproscan
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan
IPR035927 all species →	Homologous_superfamily	DUSP-like superfamily	Interproscan
IPR001394 all species →	Domain	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Interproscan
IPR028889 all species →	Domain	Ubiquitin specific protease domain	Interproscan
IPR050185 all species →	Family	Ubiquitin carboxyl-terminal hydrolase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21646 all species →	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004843 all species →	Molecular Function	cysteine-type deubiquitinase activity	Interproscan
GO:0016579 all species →	Biological Process	protein deubiquitination	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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
K11848	USP20_33; ubiquitin carboxyl-terminal hydrolase 20/33	EC:3.4.19.12	Ubiquitin system	ko04121	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_019760-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

71.2Max TPM

24.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.30	38.10
polyp at pH7 6	18	18	18.66	31.74
coral polyp · control treatment	16	16	33.11	71.23
coral polyp · oil and dispersant treatment	16	16	36.04	66.04
coral polyp · oil treatment	16	16	29.21	49.79
coral polyp · dispersant treatment	16	16	18.52	42.50
Polyp	10	10	12.67	21.87

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	-	38.10
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.05
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.06
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.86
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.02
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.74
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.21
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.95
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.72
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.02
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.87
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.23
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.34
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.15
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.74
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.82
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.67
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.20
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.15
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.11
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.04
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.89
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.33
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.91
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.04
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.41
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.21
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.90
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.73
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.50
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.94
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.28
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.23
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.07
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.19
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.87
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.46
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.58
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.25
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.68
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.41
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.15
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.05
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.41
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.70
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.85
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.37
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.46
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.04
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.69
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.60
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.92
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.78
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.22
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.73
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.06
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.89
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.41
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.58
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.92
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.58
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.79
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.37
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.70
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.60
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.91
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.30
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.38
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.89
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.62
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.61
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.23
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.25
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.13
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.18
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.46
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.89
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.50
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.10
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.39
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.29
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.08
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.47
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.52
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.85
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.13
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.75
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.20
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.53
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.71
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	21.87
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	21.05
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	16.45
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	15.58
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.85
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.68
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	10.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.37
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.67
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.08

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.