Gene detail

Detailed information of OS493_002456-T1 in Lophelia pertusa

Genomic Location: scaffold_5:2558918...2574336
NR annotation: KAJ7365740.1, Spg11p [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
Q3UHA3	Spatacsin OS=Mus musculus OX=10090 GN=Spg11 PE=1 SV=3
Q96JI7	Spatacsin OS=Homo sapiens OX=9606 GN=SPG11 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002279 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14649 all species →	Spatacsin_C	Spatacsin C-terminus	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR028103 all species →	Family	Spatacsin	Interproscan
IPR028107 all species →	Domain	Spatacsin, C-terminal domain	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_002456-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_002456-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

27.6Max TPM

14.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	17.16	26.29
polyp at pH7 6	18	18	17.25	22.79
coral polyp · control treatment	16	16	14.84	21.49
coral polyp · oil and dispersant treatment	16	16	11.99	17.19
coral polyp · oil treatment	16	16	16.60	24.61
coral polyp · dispersant treatment	16	16	12.20	27.61
Polyp	10	9	12.06	23.20

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	-	26.29
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.66
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.68
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.03
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.03
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.63
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.98
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.84
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.88
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.54
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.76
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.57
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.42
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.06
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.51
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.23
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.82
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.79
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.49
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.41
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.95
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.23
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.34
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.03
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.57
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.46
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.27
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.79
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.72
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.30
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.73
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.33
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.49
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.59
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.10
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.09
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.85
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.78
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.44
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.46
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.27
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.23
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.19
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.68
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.81
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.94
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.19
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.67
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.29
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.26
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.94
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.84
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.56
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.86
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.42
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.15
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.13
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.08
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.81
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.46
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.61
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.93
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.59
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.47
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.80
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.60
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.71
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.28
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.41
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.06
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.77
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.53
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.61
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.44
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.25
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.44
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.34
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.99
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.59
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.54
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.48
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.46
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.17
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.88
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.61
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	23.20
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	22.66
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.40
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.13
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.40
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	12.51
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.33
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.68
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.26
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.