Gene detail

Detailed information of OS493_012720-T1 in Lophelia pertusa

Genomic Location: scaffold_33:2380259...2390165
NR annotation: KAJ7379958.1, 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
PF14655 all species →	RAB3GAP2_N	Rab3 GTPase-activating protein regulatory subunit N-terminus	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR032839 all species →	Domain	Rab3-GAP regulatory subunit, N-terminal	Interproscan
IPR026059 all species →	Family	Rab3GAP regulatory subunit	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_012720-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_012720-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

108TPM > 0

7Conditions

65.7Max TPM

13.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.06	6.83
polyp at pH7 6	18	16	4.05	9.77
coral polyp · control treatment	16	16	23.82	65.72
coral polyp · oil and dispersant treatment	16	16	17.53	55.37
coral polyp · oil treatment	16	16	17.35	41.20
coral polyp · dispersant treatment	16	16	15.64	46.99
Polyp	10	10	10.99	48.15

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	-	6.83
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.89
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.86
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.33
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.32
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.16
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.05
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.05
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.05
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.92
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.79
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.57
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.54
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.48
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.46
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.48
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.77
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.45
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.28
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.33
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.93
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.13
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.72
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.29
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.29
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.17
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.03
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.97
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.94
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.75
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
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.72
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.77
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.64
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.20
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.23
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.16
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.83
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.61
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.65
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.59
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.57
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.35
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.21
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.84
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.93
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.04
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.11
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.36
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.09
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.94
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.26
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.84
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.90
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.05
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.57
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.23
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.12
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.20
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.88
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.58
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.11
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.76
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.49
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.08
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.92
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.45
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.89
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.27
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.58
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.53
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.09
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.62
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.22
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.99
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.26
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.96
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.98
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.27
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.61
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.46
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.12
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.48
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.27
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.72
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.04
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.84
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.81
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	48.15
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	22.34
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	16.09
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.29
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.06
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.14
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.06
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.85
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.90

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.