Gene detail

Detailed information of OS493_013719-T1 in Lophelia pertusa

Genomic Location: scaffold_38:424658...430169
NR annotation: KAJ7385691.1, Superoxide dismutase [Cu-Zn] [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
Q52RN5	Superoxide dismutase [Cu-Zn] OS=Bos mutus grunniens OX=30521 GN=SOD1 PE=2 SV=3
P00442	Superoxide dismutase [Cu-Zn] OS=Bos taurus OX=9913 GN=SOD1 PE=1 SV=2
P08228	Superoxide dismutase [Cu-Zn] OS=Mus musculus OX=10090 GN=Sod1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000995 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00080 all species →	Sod_Cu	Copper/zinc superoxide dismutase (SODC)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018152 all species →	Binding_site	Superoxide dismutase, copper/zinc, binding site	Interproscan
IPR036423 all species →	Homologous_superfamily	Superoxide dismutase-like, copper/zinc binding domain superfamily	Interproscan
IPR001424 all species →	Domain	Superoxide dismutase, copper/zinc binding domain	Interproscan
IPR024134 all species →	Family	Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10003 all species →	SUPEROXIDE DISMUTASE CU-ZN -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006801 all species →	Biological Process	superoxide metabolic process	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0005507 all species →	Molecular Function	copper ion binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0005777 all species →	Cellular Component	peroxisome	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	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
K04565	SOD1; superoxide dismutase, Cu-Zn family	EC:1.15.1.1	Pathways of neurodegeneration - multiple diseases	ko05022	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_013719-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

110TPM > 0

7Conditions

814.3Max TPM

426.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	624.64	814.34
polyp at pH7 6	18	18	622.17	803.99
coral polyp · control treatment	16	16	294.34	402.78
coral polyp · oil and dispersant treatment	16	16	265.43	376.66
coral polyp · oil treatment	16	16	338.48	433.02
coral polyp · dispersant treatment	16	16	261.81	621.09
Polyp	10	10	591.48	779.52

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	814.34
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	769.69
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	703.07
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	661.07
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	659.99
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	652.32
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	644.30
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	636.64
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	634.07
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	613.42
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	605.60
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	599.93
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	571.56
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	570.51
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	556.92
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	547.76
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	508.73
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	493.59
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	803.99
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	776.72
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	750.98
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	724.96
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	692.30
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	691.20
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	627.50
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	612.60
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	602.20
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	595.38
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	593.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	569.56
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	569.44
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	563.48
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	520.56
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	515.24
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	512.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	477.01
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	402.78
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	361.60
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	346.75
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	346.56
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	337.06
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	326.37
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	321.31
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	312.61
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	299.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	297.34
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	289.50
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	280.83
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	259.07
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	230.50
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	155.29
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	142.74
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	376.66
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	354.54
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	352.50
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	314.94
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	294.67
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	282.31
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	260.63
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	255.09
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	246.89
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	246.20
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	241.10
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	240.63
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	229.71
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	202.52
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	191.43
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	157.09
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	433.02
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	430.09
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	428.83
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	420.10
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	348.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	339.74
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	336.18
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	335.10
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	333.81
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	333.40
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	333.22
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	328.42
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	295.02
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	289.58
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	229.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	200.75
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	621.09
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	467.76
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	375.60
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	301.42
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	293.57
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	268.06
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	255.01
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	238.26
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	211.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	209.72
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	204.14
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	186.24
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	182.07
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	181.37
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.31
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.58
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	779.52
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	690.46
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	610.44
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	585.67
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	571.85
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	565.04
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	547.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	546.44
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	516.13
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	502.23

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.