Gene detail

Detailed information of OS493_013445-T1 in Lophelia pertusa

Genomic Location: scaffold_36:2829642...2843607
NR annotation: KAJ7336067.1, Ubiquitin carboxyl-terminal hydrolase bap1 [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
C4A0D9	Ubiquitin carboxyl-terminal hydrolase BAP1 OS=Branchiostoma floridae OX=7739 GN=BAP1 PE=3 SV=1
Q66JB6	Ubiquitin carboxyl-terminal hydrolase BAP1 OS=Xenopus tropicalis OX=8364 GN=bap1 PE=2 SV=1
D3ZHS6	Ubiquitin carboxyl-terminal hydrolase BAP1 OS=Rattus norvegicus OX=10116 GN=Bap1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004546 (this species only)
Ubiquitin family	DUB\|UCH\|UCH · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01088 all species →	Peptidase_C12	Ubiquitin carboxyl-terminal hydrolase, family 1	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan
IPR001578 all species →	Domain	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	Interproscan
IPR036959 all species →	Homologous_superfamily	Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10589 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:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0016579 all species →	Biological Process	protein deubiquitination	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
K05610	UCHL5, UCH37; ubiquitin carboxyl-terminal hydrolase L5	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_013445-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

27.9Max TPM

7.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.90	13.77
polyp at pH7 6	18	18	8.06	15.55
coral polyp · control treatment	16	16	9.71	27.91
coral polyp · oil and dispersant treatment	16	16	6.14	10.25
coral polyp · oil treatment	16	16	8.53	16.42
coral polyp · dispersant treatment	16	16	6.17	14.06
Polyp	10	10	4.41	8.06

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	-	13.77
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.87
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.72
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.22
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.12
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.53
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.22
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.17
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.17
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.74
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.46
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.02
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.45
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.40
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.67
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.26
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.58
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.56
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.20
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.80
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.58
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.54
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.39
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.89
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.65
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.96
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.80
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.34
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.05
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.91
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.37
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.57
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.09
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.72
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.33
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.52
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.85
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.77
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.92
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.13
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.44
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.53
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.42
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.25
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.94
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.64
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.37
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.26
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.58
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.89
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.63
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.26
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.03
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.74
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.23
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.81
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.51
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.84
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.28
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.42
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.59
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.97
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.25
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.12
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.08
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.52
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.13
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.98
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.97
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.01
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.60
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.97
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.87
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.06
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.78
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.61
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.72
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.49
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.70
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.17
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.74
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.97
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.58
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.58
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	8.06
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.34
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.29
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.01
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.34
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.09
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.89
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.84
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.69
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.51

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.