Gene detail

Detailed information of OS493_013718-T1 in Lophelia pertusa

Genomic Location: scaffold_38:421489...422841
NR annotation: KAJ7385690.1, 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
Q5FB29	Superoxide dismutase [Cu-Zn] OS=Capra hircus OX=9925 GN=SOD1 PE=2 SV=3
P00443	Superoxide dismutase [Cu-Zn] OS=Equus caballus OX=9796 GN=SOD1 PE=1 SV=2
Q8HXQ3	Superoxide dismutase [Cu-Zn] OS=Hylobates lar OX=9580 GN=SOD1 PE=2 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000985 (this species only) · gene tree & orthology

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
IPR001424 all species →	Domain	Superoxide dismutase, copper/zinc binding domain	Interproscan
IPR024134 all species →	Family	Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone	Interproscan
IPR036423 all species →	Homologous_superfamily	Superoxide dismutase-like, copper/zinc binding domain superfamily	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

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_013718-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_013718-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

59.7Max TPM

12.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.74	22.66
polyp at pH7 6	18	18	14.10	24.92
coral polyp · control treatment	16	16	13.24	59.75
coral polyp · oil and dispersant treatment	16	16	8.99	48.21
coral polyp · oil treatment	16	16	10.91	18.97
coral polyp · dispersant treatment	16	16	7.04	15.51
Polyp	10	9	16.15	30.15

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.66
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.93
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.54
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.14
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.90
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.42
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.72
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.14
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.74
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.59
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.36
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.52
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.23
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.11
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.90
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.84
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.48
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.18
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.92
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.50
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.21
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.85
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.67
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.69
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.01
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.58
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.04
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.45
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.07
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.06
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.64
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.63
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.08
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.32
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.92
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.18
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.75
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.63
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.20
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.86
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.89
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.54
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.49
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.49
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.52
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.27
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.40
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.15
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.71
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.79
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.28
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.21
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.40
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.40
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.27
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.51
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.19
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.97
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.94
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.78
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.44
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.15
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.03
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.98
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.97
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.05
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.51
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.97
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.70
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.62
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.36
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.10
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.80
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.34
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.33
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.27
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.85
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.96
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.44
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.10
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.91
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.73
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.02
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.52
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.18
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.38
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.70
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.02
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.01
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.32
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.88
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.38
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.08
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.55
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.43
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	30.15
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	27.31
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	23.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	23.76
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	19.28
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	16.22
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.52
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.86
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.56
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.