Gene detail

Detailed information of OS493_009170-T1 in Lophelia pertusa

Genomic Location: scaffold_22:655623...658972
NR annotation: KAJ7373848.1, Cytochrome c oxidase subunit 5B [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
Q96NR8	Retinol dehydrogenase 12 OS=Homo sapiens OX=9606 GN=RDH12 PE=1 SV=3
P59837	Retinol dehydrogenase 12 OS=Bos taurus OX=9913 GN=RDH12 PE=2 SV=1
Q8BYK4	Retinol dehydrogenase 12 OS=Mus musculus OX=10090 GN=Rdh12 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008520 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01215 all species →	COX5B	Cytochrome c oxidase subunit Vb	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002124 all species →	Family	Cytochrome c oxidase, subunit Vb	Interproscan
IPR036972 all species →	Homologous_superfamily	Cytochrome c oxidase, subunit Vb superfamily	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10122 all species →	CYTOCHROME C OXIDASE SUBUNIT 5B, MITOCHONDRIAL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005740 all species →	Cellular Component	mitochondrial envelope	Interproscan
GO:0005751 all species →	Cellular Component	obsolete mitochondrial respiratory chain complex IV	Interproscan
GO:0006123 all species →	Biological Process	mitochondrial electron transport, cytochrome c to oxygen	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_009170-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_009170-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

448.4Max TPM

99.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	102.93	124.47
polyp at pH7 6	18	18	110.42	140.33
coral polyp · control treatment	16	16	111.77	373.85
coral polyp · oil and dispersant treatment	16	16	105.83	448.43
coral polyp · oil treatment	16	16	94.41	121.78
coral polyp · dispersant treatment	16	16	59.19	81.07
Polyp	10	10	117.44	156.15

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	124.47
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	119.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	118.09
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	115.24
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	114.71
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	108.37
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	108.22
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	107.29
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	105.00
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	103.17
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	97.60
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	96.94
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	93.69
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	93.15
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	90.74
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	89.93
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	88.56
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	77.87
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	140.33
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	122.46
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	119.95
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	118.92
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	118.14
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	115.11
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	114.80
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	109.96
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	107.69
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	106.56
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	106.12
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	105.84
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	105.28
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	104.42
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	103.81
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	101.65
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	96.77
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	89.70
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	373.85
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.89
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	111.86
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	110.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	109.63
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.37
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.40
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.93
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.16
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.72
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.01
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.76
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.74
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.69
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.54
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.04
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	448.43
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	127.99
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	99.12
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.11
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	88.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.23
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.16
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.03
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.56
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.64
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.41
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.82
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.47
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.35
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.55
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.78
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	110.08
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	105.47
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	100.64
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	100.63
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.21
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	95.23
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.95
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.39
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.35
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.20
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	86.57
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	85.07
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	84.53
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.89
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.50
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.07
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.88
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.72
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.26
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.49
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.66
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.59
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.01
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.76
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.99
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.18
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.02
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.25
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.33
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.37
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.44
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	156.15
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	128.33
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	120.95
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	118.55
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	114.08
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	113.67
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	107.26
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	105.99
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	105.56
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	103.86

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.