Gene detail

Detailed information of OS493_013916-T1 in Lophelia pertusa

Genomic Location: scaffold_38:2544814...2548961
NR annotation: KAJ7385880.1, Charged multivesicular body protein 2b [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
Q6NXD2	Charged multivesicular body protein 2b OS=Danio rerio OX=7955 GN=chmp2b PE=2 SV=1
Q5F3A2	Charged multivesicular body protein 2b OS=Gallus gallus OX=9031 GN=CHMP2B PE=2 SV=1
Q9UQN3	Charged multivesicular body protein 2b OS=Homo sapiens OX=9606 GN=CHMP2B PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007822 (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
K12192	CHMP2B; charged multivesicular body protein 2B	-	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_013916-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

109TPM > 0

7Conditions

201.3Max TPM

51.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	31.52	48.26
polyp at pH7 6	18	18	34.34	40.27
coral polyp · control treatment	16	16	56.98	101.23
coral polyp · oil and dispersant treatment	16	16	80.86	118.62
coral polyp · oil treatment	16	16	50.37	72.73
coral polyp · dispersant treatment	16	16	78.45	201.27
Polyp	10	9	21.29	37.15

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.26
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.18
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.37
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.89
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.99
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.72
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.83
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.53
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.37
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.46
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.02
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.64
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.00
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.75
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.59
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.90
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.30
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.27
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.10
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.58
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.92
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.63
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.95
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.94
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.66
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.46
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.09
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.01
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.38
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.07
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.49
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.10
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.69
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.27
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.23
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.77
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.25
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.74
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.16
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.42
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.71
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.28
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.07
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.41
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.80
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.28
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.58
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.56
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.18
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.29
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	118.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	108.31
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	100.17
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.01
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.43
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.41
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.49
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	80.02
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.69
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.93
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.20
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.27
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.62
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.13
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.73
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.81
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.11
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.09
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.82
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.20
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.05
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.56
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.13
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.26
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.28
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.33
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.37
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.11
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	201.27
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.32
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	102.46
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	98.40
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.34
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.15
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.59
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.98
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.72
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.62
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.29
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.76
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.99
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.50
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.25
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.54
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	37.15
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	31.23
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	27.93
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	26.55
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	22.64
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	20.67
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.50
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	16.66
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.56
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.