Gene detail

Detailed information of OS493_002458-T1 in Lophelia pertusa

Genomic Location: scaffold_5:2598041...2600688
NR annotation: KAJ7365742.1, Spastic paraplegia 11 (autosomal recessive) [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)	OG0002279 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for OS493_002458-T1 in Lophelia pertusa.

InterPro

InterPro term	Type	Description	Source
IPR028103 all species →	Family	Spatacsin	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13650 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005737 all species →	Cellular Component	cytoplasm	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_002458-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_002458-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

101TPM > 0

7Conditions

10.4Max TPM

4.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	3.18	5.25
polyp at pH7 6	18	15	3.92	8.17
coral polyp · control treatment	16	16	4.51	10.37
coral polyp · oil and dispersant treatment	16	16	4.59	9.51
coral polyp · oil treatment	16	15	5.05	9.69
coral polyp · dispersant treatment	16	15	4.69	7.92
Polyp	10	8	1.30	3.82

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	-	5.25
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.02
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.78
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.66
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.49
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.42
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.07
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.55
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.05
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.82
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.78
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.63
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.58
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.73
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.67
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.17
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.32
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.97
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.32
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.76
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.64
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.38
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.75
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.67
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.43
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.20
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.06
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.72
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.66
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
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
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.37
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.99
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.70
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.64
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.63
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.21
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.40
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.33
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.36
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.67
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.45
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.65
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.09
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.51
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.61
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.58
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.87
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.35
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.70
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.55
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.53
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.52
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.39
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.24
SRR16706005	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	3.13
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.13
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.96
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.23
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.69
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.97
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.19
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.91
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.52
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.66
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.27
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.82
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.37
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.14
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.71
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.21
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.92
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.34
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.88
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.91
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.40
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.05
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.97
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.87
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.19
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.89
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.65
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.43
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.36
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.82
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.31
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.16
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.42
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.17
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.86
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.18
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.05
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.