Gene detail

Detailed information of OS493_002459-T1 in Lophelia pertusa

Genomic Location: scaffold_5:2600765...2609966
NR annotation: KAJ7365743.1, 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)

UniProt accession	Description
Q96JI7	Spatacsin OS=Homo sapiens OX=9606 GN=SPG11 PE=1 SV=3
Q3UHA3	Spatacsin OS=Mus musculus OX=10090 GN=Spg11 PE=1 SV=3

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_002459-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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K11579	ZWILCH; protein zwilch	-	Chromosome and associated proteins	ko03036	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_002459-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

105TPM > 0

7Conditions

8.5Max TPM

3.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	4.14	7.50
polyp at pH7 6	18	17	4.10	8.21
coral polyp · control treatment	16	16	4.46	8.19
coral polyp · oil and dispersant treatment	16	16	3.29	8.02
coral polyp · oil treatment	16	16	3.90	8.09
coral polyp · dispersant treatment	16	15	4.05	8.51
Polyp	10	9	1.06	2.53

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.50
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.49
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.31
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.01
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.80
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.40
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.38
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.33
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.74
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.69
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.67
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.39
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.27
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.92
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.83
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.72
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
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.74
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.92
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.31
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.95
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.59
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.50
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.26
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.19
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.98
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.72
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.38
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.27
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.96
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.84
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.69
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.36
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.19
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.58
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.81
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.60
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.57
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.39
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.11
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.76
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.73
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.06
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.25
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.20
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.16
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.69
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.63
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.02
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.95
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.35
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.10
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.92
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.37
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.23
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.73
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.49
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.21
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.18
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.01
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.87
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.79
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.46
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.59
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.79
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.00
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.36
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.21
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.03
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.83
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.79
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.73
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.68
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.08
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.72
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.89
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.20
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.51
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.31
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.14
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.32
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.25
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.02
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.32
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.70
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.21
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.87
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.70
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.05
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.53
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.27
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.70
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.34
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.96
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.59
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.58
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.45
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.21
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.