Gene detail

Detailed information of OS493_003917-T1 in Lophelia pertusa

Genomic Location: scaffold_8:321772...328395
NR annotation: KAJ7386957.1, Ubiquitin recognition factor in ER-associated degradation protein 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
Q92890	Ubiquitin recognition factor in ER-associated degradation protein 1 OS=Homo sapiens OX=9606 GN=UFD1 PE=1 SV=3
P70362	Ubiquitin recognition factor in ER-associated degradation protein 1 OS=Mus musculus OX=10090 GN=Ufd1 PE=1 SV=2
Q9ES53	Ubiquitin recognition factor in ER-associated degradation protein 1 OS=Rattus norvegicus OX=10116 GN=Ufd1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006228 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03152 all species →	UFD1	Ubiquitin fusion degradation protein UFD1	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004854 all species →	Family	Ubiquitin fusion degradation protein Ufd1-like	Interproscan
IPR042299 all species →	Homologous_superfamily	Ufd1-like, Nn domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12555 all species →	UBIQUITIN FUSION DEGRADATON PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0030433 all species →	Biological Process	obsolete ubiquitin-dependent ERAD pathway	Interproscan
GO:0031593 all species →	Molecular Function	polyubiquitin modification-dependent protein binding	Interproscan
GO:0034098 all species →	Cellular Component	VCP-NPL4-UFD1 AAA ATPase complex	Interproscan
GO:0071712 all species →	Biological Process	obsolete ER-associated misfolded protein catabolic process	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
K14016	UFD1; ubiquitin fusion degradation protein 1	-	Ribosome biogenesis	ko03009	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_003917-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

94.9Max TPM

33.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	28.74	44.02
polyp at pH7 6	18	18	29.10	47.45
coral polyp · control treatment	16	16	39.96	67.66
coral polyp · oil and dispersant treatment	16	16	40.47	74.52
coral polyp · oil treatment	16	16	41.74	94.87
coral polyp · dispersant treatment	16	16	18.97	30.30
Polyp	10	10	41.65	60.23

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.02
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.87
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.87
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.63
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.23
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.12
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.83
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.22
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.13
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.96
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.95
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.35
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.91
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.75
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.65
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.45
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.63
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.68
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.54
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.21
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.33
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.19
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.97
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.91
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.73
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.55
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.48
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.11
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.81
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.61
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.31
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.03
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.66
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.85
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.85
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.63
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.90
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.41
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.37
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.85
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.68
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.67
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.47
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.04
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.85
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.29
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.49
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.36
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.52
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.34
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.68
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.80
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.21
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.65
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.52
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.99
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.67
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.69
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.59
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.18
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.66
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.37
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.43
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	94.87
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.43
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.20
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.04
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.46
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.61
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.72
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.97
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.70
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.18
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.82
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.24
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.85
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.11
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.30
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.99
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.33
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.38
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.33
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.11
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.25
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.05
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.65
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.08
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.31
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.23
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.15
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.81
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.42
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.11
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	60.23
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	52.94
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	51.91
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	50.06
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	47.74
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	36.99
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	34.45
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	30.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	29.50
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	22.27

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.