Gene detail

Detailed information of OS493_035884-T1 in Lophelia pertusa

Genomic Location: scaffold_338:114237...130635
NR annotation: KAJ7382303.1, Ubiquitin carboxyl-terminal hydrolase 25 [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
Q9UHP3	Ubiquitin carboxyl-terminal hydrolase 25 OS=Homo sapiens OX=9606 GN=USP25 PE=1 SV=4
P57080	Ubiquitin carboxyl-terminal hydrolase 25 OS=Mus musculus OX=10090 GN=Usp25 PE=1 SV=2
Q96RU2	Ubiquitin carboxyl-terminal hydrolase 28 OS=Homo sapiens OX=9606 GN=USP28 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008253 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00443 all species →	UCH	Ubiquitin carboxyl-terminal hydrolase	Family	Interproscan
PF02809 all species →	UIM	Ubiquitin interaction motif	Motif	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003903 all species →	Conserved_site	Ubiquitin interacting motif	Interproscan
IPR001394 all species →	Domain	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Interproscan
IPR028889 all species →	Domain	Ubiquitin specific protease domain	Interproscan
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan
IPR044635 all species →	Family	Ubiquitin carboxyl-terminal hydrolase 14-like	Interproscan
IPR018200 all species →	Conserved_site	Ubiquitin specific protease, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43982 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:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0061136 all species →	Biological Process	regulation of proteasomal protein catabolic process	Interproscan
GO:0070628 all species →	Molecular Function	proteasome binding	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_035884-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_035884-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

60.2Max TPM

24.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.34	26.08
polyp at pH7 6	18	18	22.07	27.35
coral polyp · control treatment	16	16	33.87	60.15
coral polyp · oil and dispersant treatment	16	16	32.60	55.04
coral polyp · oil treatment	16	16	26.36	42.40
coral polyp · dispersant treatment	16	16	17.45	30.52
Polyp	10	10	12.64	24.31

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.08
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.12
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.77
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.76
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.76
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.19
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.87
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.60
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.06
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.77
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.64
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.36
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.63
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.83
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.74
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.46
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.40
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.08
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.28
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.20
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.28
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.02
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.61
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.54
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.46
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.77
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.68
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.44
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.16
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.32
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.31
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.98
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.32
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.44
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.15
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.82
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.47
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.20
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.81
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.82
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.85
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.32
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.94
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.65
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.02
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.00
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.49
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.30
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.70
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.04
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.11
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.68
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.38
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.18
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.74
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.20
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.19
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.33
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.24
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.78
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.18
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.73
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.44
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.60
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.49
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.31
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.64
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.27
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.71
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.70
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.40
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.31
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.13
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.43
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.41
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.05
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.34
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.52
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.07
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.72
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.92
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.54
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.80
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.01
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.84
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.59
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.28
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.20
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.99
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.93
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.76
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.76
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	24.31
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	20.09
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	15.90
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	11.54
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.05
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.83
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.80
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.60
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.55
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.76

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.