Gene detail

Detailed information of OS493_012718-T1 in Lophelia pertusa

Genomic Location: scaffold_33:2341093...2370433
NR annotation: KAJ7379956.1, Rab3 GTPase-activating protein non-catalytic subunit [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
Q9H2M9	Rab3 GTPase-activating protein non-catalytic subunit OS=Homo sapiens OX=9606 GN=RAB3GAP2 PE=1 SV=1
Q8BMG7	Rab3 GTPase-activating protein non-catalytic subunit OS=Mus musculus OX=10090 GN=Rab3gap2 PE=1 SV=2
Q5U1Z0	Rab3 GTPase-activating protein non-catalytic subunit OS=Rattus norvegicus OX=10116 GN=Rab3gap2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003135 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14656 all species →	RAB3GAP2_C	Rab3 GTPase-activating protein regulatory subunit C-terminus	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR026059 all species →	Family	Rab3GAP regulatory subunit	Interproscan
IPR029257 all species →	Domain	Rab3GAP regulatory subunit, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12472 all species →	RAB3-GAP REGULATORY DOMAIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0043087 all species →	Biological Process	regulation of GTPase activity	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_012718-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_012718-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

111.5Max TPM

23.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.01	14.83
polyp at pH7 6	18	18	10.94	17.68
coral polyp · control treatment	16	16	36.82	98.26
coral polyp · oil and dispersant treatment	16	16	27.09	66.28
coral polyp · oil treatment	16	16	33.73	68.27
coral polyp · dispersant treatment	16	16	23.24	62.36
Polyp	10	10	27.29	111.54

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.83
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.34
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.20
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.91
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.34
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.14
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.96
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.67
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.83
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.64
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.11
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.35
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.70
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.61
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.53
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.12
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.68
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.23
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.10
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.66
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.63
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.62
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.23
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.42
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.81
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.72
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.13
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.65
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.97
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.45
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.13
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	98.26
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.16
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.44
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.74
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.99
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.30
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.49
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.04
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.72
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.44
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.04
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.98
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.80
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.26
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.08
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.34
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.28
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.89
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.53
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.85
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.40
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.12
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.20
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.28
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.63
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.45
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.99
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.19
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.27
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.94
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.71
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.99
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.77
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.06
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.88
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.87
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.19
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.84
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.22
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.80
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.67
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.41
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.56
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.44
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.45
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.47
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.25
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.80
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.02
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.43
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.23
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.19
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.03
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.78
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.68
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.48
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	111.54
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	44.04
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	24.60
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.01
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	15.82
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	13.76
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.49
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.18
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.49
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.94

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.