Gene detail

Detailed information of OS493_011939-T1 in Lophelia pertusa

Genomic Location: scaffold_30:3431165...3436863
NR annotation: KAJ7336717.1, ESCRT III complex subunit vps24 [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
Q6NRM7	Charged multivesicular body protein 3 OS=Xenopus laevis OX=8355 GN=chmp3 PE=2 SV=3
Q5BKM3	Charged multivesicular body protein 3 OS=Xenopus tropicalis OX=8364 GN=chmp3 PE=2 SV=4
Q8CGS4	Charged multivesicular body protein 3 OS=Rattus norvegicus OX=10116 GN=Chmp3 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007242 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03357 all species →	Snf7	Snf7	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005024 all species →	Family	Snf7 family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10476 all species →	CHARGED MULTIVESICULAR BODY PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0007034 all species →	Biological Process	vacuolar transport	Interproscan
GO:0000815 all species →	Cellular Component	ESCRT III complex	Interproscan
GO:0005771 all species →	Cellular Component	multivesicular body	Interproscan
GO:0015031 all species →	Biological Process	protein transport	Interproscan
GO:0032509 all species →	Biological Process	endosome transport via multivesicular body sorting pathway	Interproscan
GO:0045324 all species →	Biological Process	late endosome to vacuole transport	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
K12193	VPS24, CHMP3; charged multivesicular body protein 3	-	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_011939-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

129.3Max TPM

47.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	33.05	53.54
polyp at pH7 6	18	18	35.45	46.87
coral polyp · control treatment	16	16	55.85	88.51
coral polyp · oil and dispersant treatment	16	16	69.34	87.87
coral polyp · oil treatment	16	16	47.23	61.10
coral polyp · dispersant treatment	16	16	61.64	129.34
Polyp	10	10	23.33	34.32

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	-	53.54
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.13
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.92
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.42
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.51
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.35
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.16
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.89
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.11
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.68
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.49
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.56
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.79
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.27
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.87
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.69
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.01
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.82
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.21
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.01
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.75
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.32
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.20
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.69
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.93
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.32
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.38
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.80
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.35
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	88.51
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.23
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.18
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.68
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.58
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.46
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.45
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.40
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.21
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.87
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.41
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.64
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.42
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.38
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.86
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.32
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.87
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.75
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.62
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.87
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.58
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.16
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.96
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.37
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.49
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.70
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.32
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.01
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.90
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.68
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.10
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.59
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.81
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.40
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.96
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.04
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.33
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.87
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.31
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.72
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.68
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.01
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.15
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.17
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	129.34
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.33
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.07
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	77.19
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.64
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.43
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.23
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.85
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.41
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.83
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.55
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.62
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.33
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.98
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.75
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.68
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	34.32
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	31.75
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	24.57
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	24.54
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	23.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	22.22
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	22.20
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	20.22
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.65
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.64

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.