Gene detail

Detailed information of OS493_001075-T1 in Lophelia pertusa

Genomic Location: scaffold_2:3884808...3895697
NR annotation: KAJ7387732.1, Vacuolar protein-sorting-associated protein 28 [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
Q3T178	Vacuolar protein sorting-associated protein 28 homolog OS=Bos taurus OX=9913 GN=VPS28 PE=2 SV=1
Q9D1C8	Vacuolar protein sorting-associated protein 28 homolog OS=Mus musculus OX=10090 GN=Vps28 PE=1 SV=1
B5DEN9	Vacuolar protein sorting-associated protein 28 homolog OS=Rattus norvegicus OX=10116 GN=Vps28 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007231 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03997 all species →	VPS28	VPS28 protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038358 all species →	Homologous_superfamily	VPS28, N-terminal domain superfamily	Interproscan
IPR007143 all species →	Family	Vacuolar protein sorting-associated Vps28	Interproscan
IPR037206 all species →	Homologous_superfamily	VPS28, C-terminal domain superfamily	Interproscan
IPR017899 all species →	Domain	Vacuolar protein sorting-associated, VPS28, C-terminal	Interproscan
IPR017898 all species →	Domain	Vacuolar protein sorting-associated, VPS28, N-terminal	Interproscan
IPR037202 all species →	Homologous_superfamily	ESCRT assembly domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12937 all species →	VACUOLAR PROTEIN SORTING 28, ISOFORM 2 VPS28	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000813 all species →	Cellular Component	ESCRT I complex	Interproscan
GO:0032509 all species →	Biological Process	endosome transport via multivesicular body sorting pathway	Interproscan
GO:0043328 all species →	Biological Process	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	Interproscan
GO:0044877 all species →	Molecular Function	protein-containing complex 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
K12184	VPS28; ESCRT-I complex subunit VPS28	-	Exosome	ko04147	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_001075-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

53.2Max TPM

28.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	25.75	40.20
polyp at pH7 6	18	18	27.43	42.50
coral polyp · control treatment	16	16	33.58	50.63
coral polyp · oil and dispersant treatment	16	16	28.06	33.49
coral polyp · oil treatment	16	16	32.75	45.80
coral polyp · dispersant treatment	16	16	23.14	36.08
Polyp	10	10	32.08	53.21

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.20
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.45
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.31
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.98
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.54
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.77
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.72
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.35
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.91
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.42
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.09
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.64
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.99
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.66
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.37
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.50
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.85
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.28
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.84
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.90
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.72
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.27
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.91
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.44
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.25
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.11
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.03
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.83
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.98
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.05
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.87
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.63
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.38
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.90
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.97
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.03
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.05
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.99
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.14
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.30
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.94
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.49
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.89
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.53
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.23
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.51
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.31
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.82
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.69
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.04
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.89
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.16
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.98
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.34
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.32
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.86
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.64
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.78
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.75
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.30
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.53
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.80
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.58
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.06
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.13
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.93
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.60
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.35
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.68
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.14
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.06
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.27
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.62
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.20
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.72
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.08
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.43
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.45
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.35
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.74
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.66
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.10
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.58
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.99
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.71
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.56
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.56
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.11
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.71
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	53.21
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	39.75
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	38.57
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	38.53
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	31.80
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	26.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	23.88
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	23.13
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	22.60
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	22.40

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.