Gene detail

Detailed information of OS493_001974-T1 in Lophelia pertusa

Genomic Location: scaffold_4:3444877...3456557
NR annotation: KAJ7375230.1, Rab-like protein 6 [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
Q5U3K5	Rab-like protein 6 OS=Mus musculus OX=10090 GN=Rabl6 PE=1 SV=2
Q3YEC7	Rab-like protein 6 OS=Homo sapiens OX=9606 GN=RABL6 PE=1 SV=2
Q08DA0	Rab-like protein 6 OS=Bos taurus OX=9913 GN=RABL6 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003730 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00071 all species →	Ras	Ras family	Domain	Interproscan
PF08477 all species →	Roc	Ras of Complex, Roc, domain of DAPkinase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001806 all species →	Family	Small GTPase	Interproscan
IPR040385 all species →	Family	Rab-like protein 6	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14932 all species →	RAS GTPASE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	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_001974-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_001974-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

28.1Max TPM

12.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.06	16.47
polyp at pH7 6	18	18	10.88	19.09
coral polyp · control treatment	16	16	15.35	28.08
coral polyp · oil and dispersant treatment	16	16	12.07	20.75
coral polyp · oil treatment	16	16	14.13	22.52
coral polyp · dispersant treatment	16	16	11.98	18.54
Polyp	10	9	11.09	20.07

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.47
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.17
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.19
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.52
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.66
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.49
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.43
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.39
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.03
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.49
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.35
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.64
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.71
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.62
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.90
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.83
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.56
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.09
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.42
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.85
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.49
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.83
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.59
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.10
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.25
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.47
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.43
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.19
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.18
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.34
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.14
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.69
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.50
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.94
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.08
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.41
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.17
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.90
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.59
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.12
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.89
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.75
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.99
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.87
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.59
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.35
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.17
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.96
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.75
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.18
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.85
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.91
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.56
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.33
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.61
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.20
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.18
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.64
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.08
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.76
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.67
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.65
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.52
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.44
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.73
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.24
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.50
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.23
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.88
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.60
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.54
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.37
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.31
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.66
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.29
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.80
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.64
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.33
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.54
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.15
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.01
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.19
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.81
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.45
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.33
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.35
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.03
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.90
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.88
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.30
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.67
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.18
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.98
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	20.07
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	18.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	16.26
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	15.28
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.80
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.29
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.23
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.93
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.85
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.