Gene detail

Detailed information of OS493_005217-T1 in Lophelia pertusa

Genomic Location: scaffold_10:4069113...4079767
NR annotation: KAJ7374864.1, hypothetical protein OS493_005217 [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
Q6P6Y1	RAB11-binding protein RELCH homolog OS=Danio rerio OX=7955 GN=relch PE=2 SV=1
Q148V7	RAB11-binding protein RELCH OS=Mus musculus OX=10090 GN=Relch PE=1 SV=1
Q08BT5	RAB11-binding protein RELCH homolog OS=Xenopus tropicalis OX=8364 GN=relch PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004191 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02985 all species →	HEAT	HEAT repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR040362 all species →	Family	RAB11-binding protein RELCH	Interproscan
IPR000357 all species →	Repeat	HEAT repeat	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR021133 all species →	Repeat	HEAT, type 2	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32059 all species →	RAB11-BINDING PROTEIN RELCH	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0032367 all species →	Biological Process	intracellular cholesterol transport	Interproscan
GO:0055037 all species →	Cellular Component	recycling endosome	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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_005217-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_005217-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

15.3Max TPM

6.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.97	6.97
polyp at pH7 6	18	17	5.17	6.98
coral polyp · control treatment	16	16	9.63	15.34
coral polyp · oil and dispersant treatment	16	16	6.27	10.11
coral polyp · oil treatment	16	16	7.75	12.69
coral polyp · dispersant treatment	16	16	5.54	11.18
Polyp	10	10	3.35	7.16

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.97
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.81
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.34
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.90
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.71
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.58
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.97
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.57
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.52
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.45
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.39
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.37
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.33
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.28
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.29
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.09
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.98
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.95
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.67
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.61
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.95
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.92
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.85
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.84
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.65
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.59
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.51
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.16
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.35
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.15
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.98
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.27
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.34
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.93
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.96
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.64
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.16
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.84
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.51
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.37
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.83
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.11
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.46
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.96
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.18
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.11
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.79
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.34
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.16
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.04
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.77
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.59
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.21
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.98
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.89
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.38
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.10
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.84
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.59
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.69
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.17
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.35
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.18
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.64
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.32
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.95
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.41
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.90
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.80
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.04
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.89
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.87
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.57
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.55
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.73
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.18
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.74
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.64
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.02
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.92
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.09
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.93
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.77
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.47
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.80
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.24
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.94
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.14
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.54
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.18
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.16
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.67
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.98
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.06
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.99
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.02
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.74
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.56

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.