Gene detail

Detailed information of OS493_002401-T1 in Lophelia pertusa

Genomic Location: scaffold_5:1699212...1716059
NR annotation: KAJ7365686.1, Ubiquilin-1 [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
Q99NB8	Ubiquilin-4 OS=Mus musculus OX=10090 GN=Ubqln4 PE=1 SV=1
Q9UHD9	Ubiquilin-2 OS=Homo sapiens OX=9606 GN=UBQLN2 PE=1 SV=2
Q8R317	Ubiquilin-1 OS=Mus musculus OX=10090 GN=Ubqln1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005232 (this species only)
Ubiquitin family	ULD\|UBL\|NEDD8 · all ubiquitin genes in this species
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_Other · all ubiquitin genes in this species
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_PIM · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00240 all species →	ubiquitin	Ubiquitin family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000626 all species →	Domain	Ubiquitin-like domain	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan
IPR006636 all species →	Domain	Heat shock chaperonin-binding	Interproscan
IPR015496 all species →	Family	Ubiquilin	Interproscan
IPR019956 all species →	Domain	Ubiquitin domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10677 all species →	UBIQUILIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0031593 all species →	Molecular Function	polyubiquitin modification-dependent protein 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K04523	UBQLN, DSK2; ubiquilin	-	Proteasome	ko03051	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_002401-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

66.8Max TPM

22.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.65	22.76
polyp at pH7 6	18	18	15.14	22.35
coral polyp · control treatment	16	16	29.32	59.71
coral polyp · oil and dispersant treatment	16	16	34.23	54.15
coral polyp · oil treatment	16	16	20.07	41.99
coral polyp · dispersant treatment	16	16	30.18	66.80
Polyp	10	10	8.01	12.27

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	-	22.76
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.93
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.14
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.04
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.33
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.13
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.69
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.60
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.24
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.67
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.54
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.33
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.83
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.36
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.25
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.58
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.35
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.87
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.41
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.58
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.64
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.44
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.84
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.85
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.66
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.95
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.84
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.71
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.94
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.37
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.68
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.54
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.71
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.52
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.18
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.71
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.39
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.59
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.99
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.43
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.35
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.60
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.19
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.13
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.79
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.93
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.44
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.25
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.15
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.86
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.73
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.44
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.83
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.44
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.24
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.18
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.40
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.44
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.28
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.92
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.86
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.63
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.11
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.24
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.99
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.18
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.95
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.18
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.64
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.35
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.08
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.03
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.01
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.26
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.74
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.50
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.30
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.86
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.80
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.76
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.74
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.83
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.31
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.86
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.75
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.39
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.23
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.81
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.55
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.48
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.01
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.35
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.11
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.27
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.94
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	11.58
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.83
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.06
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.91
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.78
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.72
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.35
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.69

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.