Gene detail

Detailed information of OS493_004360-T1 in Lophelia pertusa

Genomic Location: scaffold_8:5601004...5608618
NR annotation: KAJ7387366.1, melanosome assembly [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005674 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF19031 all species →	Intu_longin_1	First Longin domain of INTU, CCZ1 and HPS4	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR043987 all species →	Domain	CCZ1/INTU/HSP4, first Longin domain	Interproscan
IPR026091 all species →	Family	BLOC-3 complex member HPS4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14407 all species →	HERMANSKY-PUDLAK SYNDROME 4 PROTEIN LIGHT-EAR PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005765 all species →	Cellular Component	lysosomal membrane	Interproscan
GO:0006605 all species →	Biological Process	protein targeting	Interproscan
GO:0017137 all species →	Molecular Function	small GTPase binding	Interproscan
GO:0031085 all species →	Cellular Component	BLOC-3 complex	Interproscan
GO:0031410 all species →	Cellular Component	cytoplasmic vesicle	Interproscan
GO:1903232 all species →	Biological Process	melanosome assembly	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_004360-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_004360-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

7.9Max TPM

3.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.36	5.13
polyp at pH7 6	18	17	2.87	4.20
coral polyp · control treatment	16	16	4.69	7.39
coral polyp · oil and dispersant treatment	16	16	4.25	7.92
coral polyp · oil treatment	16	16	3.64	7.65
coral polyp · dispersant treatment	16	15	2.70	6.61
Polyp	10	10	1.87	4.57

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.13
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.82
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.50
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.32
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.32
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.08
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.80
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.60
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.56
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.94
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.93
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.85
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.51
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.37
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.83
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.80
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.58
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.20
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.92
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.92
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.83
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.58
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.53
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.48
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.48
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.25
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.56
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.46
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.31
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.16
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.66
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.39
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.33
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.32
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.27
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.19
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.36
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.25
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.19
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.09
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.06
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.24
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.56
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.18
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.13
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.74
SRR16705977	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	7.30
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.98
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.57
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.10
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.96
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.08
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.70
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.65
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.25
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.22
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.88
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.43
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.60
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.07
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.82
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.50
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.19
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.14
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.06
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.38
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.86
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.81
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.14
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.01
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.88
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.36
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.82
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.61
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.48
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.28
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.01
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.59
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.69
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.54
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.14
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.01
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.78
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.39
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.08
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.88
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.53
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.57
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.29
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.59
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.39
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.30
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.20
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.95
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.63
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.49
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.26

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.