Gene detail

Detailed information of OS493_010654-T1 in Lophelia pertusa

Genomic Location: scaffold_26:1789388...1812367
NR annotation: KAJ7386250.1, Mitochondrial Rho GTPase 2 [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
Q6NVC5	Mitochondrial Rho GTPase 1-A OS=Danio rerio OX=7955 GN=rhot1a PE=2 SV=1
Q8BG51	Mitochondrial Rho GTPase 1 OS=Mus musculus OX=10090 GN=Rhot1 PE=1 SV=1
A1L1L6	Mitochondrial Rho GTPase OS=Rattus norvegicus OX=10116 GN=Rhot1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003988 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00071 all species →	Ras	Ras family	Domain	Interproscan
PF08355 all species →	EF_assoc_1	EF hand associated	Family	Interproscan
PF08356 all species →	EF_assoc_2	EF hand associated	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002048 all species →	Domain	EF-hand domain	Interproscan
IPR001806 all species →	Family	Small GTPase	Interproscan
IPR021181 all species →	Family	Mitochondrial Rho GTPase	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR018247 all species →	Binding_site	EF-Hand 1, calcium-binding site	Interproscan
IPR013566 all species →	Domain	Mitochondrial Rho GTPase 1/3, EF hand associated, type-1	Interproscan
IPR013567 all species →	Domain	EF hand associated, type-2	Interproscan
IPR003578 all species →	Family	Small GTPase Rho	Interproscan
IPR005225 all species →	Domain	Small GTP-binding protein domain	Interproscan
IPR011992 all species →	Homologous_superfamily	EF-hand domain pair	Interproscan
IPR020860 all species →	Domain	MIRO domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24072 all species →	RHO FAMILY GTPASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0005741 all species →	Cellular Component	mitochondrial outer membrane	Interproscan
GO:0007005 all species →	Biological Process	mitochondrion organization	Interproscan
GO:0007264 all species →	Biological Process	small GTPase-mediated signal transduction	Interproscan
GO:0031307 all species →	Cellular Component	obsolete integral component of mitochondrial outer membrane	Interproscan
GO:0047497 all species →	Biological Process	mitochondrion transport along microtubule	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_010654-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_010654-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

79.0Max TPM

16.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.35	18.45
polyp at pH7 6	18	18	14.41	24.83
coral polyp · control treatment	16	16	23.37	78.95
coral polyp · oil and dispersant treatment	16	16	17.51	52.48
coral polyp · oil treatment	16	16	20.30	36.91
coral polyp · dispersant treatment	16	16	14.10	24.66
Polyp	10	10	12.63	21.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.45
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.58
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.21
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.38
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.81
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.23
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.67
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.02
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.38
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.37
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.29
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.15
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.88
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.65
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.26
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.21
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.56
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.83
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.80
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.76
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.09
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.88
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.79
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.73
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.48
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.07
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.05
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.37
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.24
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.10
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.79
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.69
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.04
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.93
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.95
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.04
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.78
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.60
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.61
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.86
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.66
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.77
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.00
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.84
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.90
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.81
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.40
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.13
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.17
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.48
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.53
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.78
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.39
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.34
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.60
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.01
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.20
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.12
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.54
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.35
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.40
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.66
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.51
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.91
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.49
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.72
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.46
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.26
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.29
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.23
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.95
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.17
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.84
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.16
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.68
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.52
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.31
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.66
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.89
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.72
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.02
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.38
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.74
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.44
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.66
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.59
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.93
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.67
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.89
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.87
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	21.18
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.01
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	18.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.85
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	13.99
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.10
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.70
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.91
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.20

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.