Gene detail

Detailed information of OS493_039343-T1 in Lophelia pertusa

Genomic Location: scaffold_1079:10684...15102
NR annotation: KAJ7348742.1, Charged multivesicular body protein 2A, partial [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
O43633	Charged multivesicular body protein 2a OS=Homo sapiens OX=9606 GN=CHMP2A PE=1 SV=1
Q9DB34	Charged multivesicular body protein 2a OS=Mus musculus OX=10090 GN=Chmp2a PE=1 SV=1
Q6IP52	Charged multivesicular body protein 2a OS=Xenopus laevis OX=8355 GN=chmp2a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007574 (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

No KEGG orthology assignment for OS493_039343-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_039343-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

88TPM > 0

7Conditions

185.3Max TPM

24.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	10	5.28	31.70
polyp at pH7 6	18	6	3.73	14.63
coral polyp · control treatment	16	16	26.05	66.18
coral polyp · oil and dispersant treatment	16	16	48.83	101.29
coral polyp · oil treatment	16	16	19.43	40.80
coral polyp · dispersant treatment	16	16	54.38	185.26
Polyp	10	8	10.45	22.11

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.70
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.94
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.89
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.79
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.51
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.21
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.03
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.46
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.63
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.85
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.31
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.69
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.59
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.10
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.18
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.41
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.15
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.47
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.92
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.90
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.76
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.77
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.13
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.09
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.64
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.99
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.45
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.98
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.29
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	99.64
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	93.08
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.11
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.61
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.71
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.09
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.78
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.93
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.93
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.31
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.73
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.56
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.10
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.53
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.86
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.80
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.09
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.65
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.03
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.12
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.75
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.55
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.69
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.69
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.49
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.49
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.95
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.95
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.59
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.65
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	185.26
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	101.81
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	93.23
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	77.21
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.14
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.03
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.43
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.76
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.12
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.35
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.39
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.47
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.90
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.42
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.67
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	22.11
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	20.56
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	19.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	15.33
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.15
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.93
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.25
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.07
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.