Gene detail

Detailed information of OS493_015627-T1 in Lophelia pertusa

Genomic Location: scaffold_47:1152204...1156747
NR annotation: KAJ7360525.1, Charged multivesicular body protein 1A [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
Q6PHF0	Charged multivesicular body protein 1a OS=Danio rerio OX=7955 GN=chmp1a PE=2 SV=1
Q921W0	Charged multivesicular body protein 1a OS=Mus musculus OX=10090 GN=Chmp1a PE=1 SV=1
Q9HD42	Charged multivesicular body protein 1a OS=Homo sapiens OX=9606 GN=CHMP1A PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002039 (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:0000815 all species →	Cellular Component	ESCRT III complex	Interproscan
GO:0005771 all species →	Cellular Component	multivesicular body	Interproscan
GO:0007034 all species →	Biological Process	vacuolar transport	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
K12197	CHMP1, VPS46, DID2; charged multivesicular body protein 1	-	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_015627-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

200.4Max TPM

64.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	36.99	52.49
polyp at pH7 6	18	18	45.57	69.81
coral polyp · control treatment	16	16	73.17	124.64
coral polyp · oil and dispersant treatment	16	16	86.50	145.89
coral polyp · oil treatment	16	16	54.41	80.43
coral polyp · dispersant treatment	16	16	112.77	200.39
Polyp	10	10	39.43	70.07

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.49
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.36
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.50
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.58
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.18
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.25
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.70
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.98
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.62
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.81
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.88
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.33
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.97
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.59
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.20
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.10
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.92
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.76
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.08
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.84
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.74
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.93
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.81
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.02
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.33
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.79
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.88
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.94
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.77
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.33
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.68
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.31
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.66
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.48
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	124.64
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	116.10
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	100.72
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	100.48
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.62
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.29
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.17
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.82
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.11
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.85
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.76
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.62
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.50
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.51
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	145.89
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	123.03
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	103.82
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	97.87
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	97.16
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.46
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	94.48
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.43
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.61
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.92
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.72
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.69
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.94
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.65
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.79
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.43
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.18
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.91
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.97
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.63
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.48
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.57
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.05
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.97
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.82
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.26
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.28
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.79
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.18
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	200.39
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	177.87
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	169.49
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	157.69
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	150.51
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	135.88
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	135.21
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	117.91
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	104.47
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.99
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	98.71
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.44
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	80.44
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.97
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.80
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.56
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	70.07
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	65.01
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	50.42
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	44.83
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	43.69
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	37.53
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	27.48
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	27.27
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	16.41
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.60

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.