Gene detail

Detailed information of OS493_022158-T1 in Lophelia pertusa

Genomic Location: scaffold_89:1321561...1326114
NR annotation: KAJ7358714.1, hypothetical protein OS493_022158 [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
Q9WU84	Copper chaperone for superoxide dismutase OS=Mus musculus OX=10090 GN=Ccs PE=1 SV=1
Q9JK72	Copper chaperone for superoxide dismutase OS=Rattus norvegicus OX=10116 GN=Ccs PE=1 SV=1
Q6PWT7	Copper chaperone for superoxide dismutase OS=Sus scrofa OX=9823 GN=CCS PE=2 SV=1

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
GO:0016532 all species →	Molecular Function	superoxide dismutase copper chaperone activity	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
K04569	CCS; copper chaperone for superoxide dismutase	-	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_022158-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

63.9Max TPM

25.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	28.83	49.00
polyp at pH7 6	18	18	27.85	40.05
coral polyp · control treatment	16	16	30.07	49.32
coral polyp · oil and dispersant treatment	16	16	23.95	63.86
coral polyp · oil treatment	16	16	28.96	38.26
coral polyp · dispersant treatment	16	16	17.31	35.80
Polyp	10	9	16.43	27.81

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.24
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.95
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.89
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.49
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.90
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.24
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.60
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.20
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.20
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.15
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.31
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.51
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.30
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.17
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.09
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.93
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.83
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.05
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.39
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.91
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.86
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.02
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.88
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.10
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.03
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.34
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.27
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.71
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.07
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.98
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.30
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.24
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.65
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.49
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.98
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.32
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.46
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.94
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.56
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.09
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.33
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.86
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.21
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.66
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.41
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.93
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.70
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.61
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.67
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.36
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.86
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.56
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.92
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.77
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.77
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.83
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.58
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.02
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.01
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.27
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.15
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.38
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.02
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.78
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.72
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.26
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.91
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.84
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.53
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.40
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.62
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.03
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.77
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.88
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.09
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.66
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.40
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.88
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.12
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.09
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.94
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.80
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.92
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.19
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.99
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.95
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.20
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.50
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.39
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.13
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.77
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.05
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.58
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.21
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.21
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	27.81
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	27.52
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	25.05
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	23.47
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	22.36
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	12.53
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.28
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.14
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.10
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.