Gene detail

Detailed information of OS493_004521-T1 in Lophelia pertusa

Genomic Location: scaffold_9:1079563...1086372
NR annotation: KAJ7380934.1, Deubiquitinating protein VCIP135 [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
Q8CF97	Deubiquitinating protein VCPIP1 OS=Rattus norvegicus OX=10116 GN=Vcpip1 PE=1 SV=2
Q96JH7	Deubiquitinating protein VCPIP1 OS=Homo sapiens OX=9606 GN=VCPIP1 PE=1 SV=2
Q8CDG3	Deubiquitinating protein VCPIP1 OS=Mus musculus OX=10090 GN=Vcpip1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006707 (this species only)
Ubiquitin family	DUB\|OTU\|OTU · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF19437 all species →	VCIP135_N	VCIP135 N-terminal	Domain	Interproscan
PF02338 all species →	OTU	OTU-like cysteine protease	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039087 all species →	Family	Deubiquitinating protein VCPIP1	Interproscan
IPR045827 all species →	Domain	Deubiquitinating protein VCPIP1, N-terminal	Interproscan
IPR003323 all species →	Domain	OTU domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14843 all species →	DEUBIQUITINATING PROTEIN VCIP135	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004843 all species →	Molecular Function	cysteine-type deubiquitinase activity	Interproscan
GO:0016320 all species →	Biological Process	endoplasmic reticulum membrane fusion	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0035871 all species →	Biological Process	protein K11-linked deubiquitination	Interproscan
GO:0071108 all species →	Biological Process	protein K48-linked deubiquitination	Interproscan
GO:0090168 all species →	Biological Process	Golgi reassembly	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_004521-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_004521-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

22.7Max TPM

9.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.99	22.67
polyp at pH7 6	18	18	9.84	16.17
coral polyp · control treatment	16	16	12.97	21.99
coral polyp · oil and dispersant treatment	16	16	9.85	17.16
coral polyp · oil treatment	16	16	10.39	16.30
coral polyp · dispersant treatment	16	16	7.93	15.78
Polyp	10	10	3.11	6.23

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.67
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.84
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.17
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.17
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.86
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.51
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.15
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.65
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.15
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.74
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.83
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.79
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.19
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.74
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.66
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.06
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.15
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.45
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.17
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.63
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.39
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.12
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.62
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.84
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.77
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.14
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.31
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.86
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.82
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.25
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.28
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.11
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.70
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.17
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.04
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.93
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.99
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.22
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.36
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.21
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.87
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.22
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.40
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.55
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.02
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.82
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.66
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.72
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.11
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.09
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.66
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.65
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.81
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.53
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.25
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.72
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.20
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.75
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.11
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.25
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.72
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.61
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.45
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.32
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.88
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.90
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.30
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.20
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.23
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.92
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.60
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.24
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.01
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.29
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.48
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.98
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.96
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.08
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.55
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.98
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.54
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.78
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.12
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.08
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.75
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.16
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.92
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.91
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.41
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.95
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.65
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.41
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.45
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.75
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.68
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.40
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.23
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.92
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.09
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.77
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.30
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.69
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.11
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.83

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.