Gene detail

Detailed information of OS493_029973-T1 in Lophelia pertusa

Genomic Location: scaffold_187:420650...423468
NR annotation: KAJ7389634.1, hypothetical protein OS493_029973 [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
Q6UPE0	Choline dehydrogenase, mitochondrial OS=Rattus norvegicus OX=10116 GN=Chdh PE=1 SV=1
Q8BJ64	Choline dehydrogenase, mitochondrial OS=Mus musculus OX=10090 GN=Chdh PE=1 SV=1
Q8NE62	Choline dehydrogenase, mitochondrial OS=Homo sapiens OX=9606 GN=CHDH PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001469 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05199 all species →	GMC_oxred_C	GMC oxidoreductase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036188 all species →	Homologous_superfamily	FAD/NAD(P)-binding domain superfamily	Interproscan
IPR012132 all species →	Family	Glucose-methanol-choline oxidoreductase	Interproscan
IPR007867 all species →	Domain	Glucose-methanol-choline oxidoreductase, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11552 all species →	GLUCOSE-METHANOL-CHOLINE GMC OXIDOREDUCTASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005743 all species →	Cellular Component	mitochondrial inner membrane	Interproscan
GO:0008812 all species →	Molecular Function	choline dehydrogenase activity	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0016614 all species →	Molecular Function	oxidoreductase activity, acting on CH-OH group of donors	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_029973-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_029973-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

99TPM > 0

7Conditions

17.8Max TPM

3.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.88	13.08
polyp at pH7 6	18	18	7.35	17.76
coral polyp · control treatment	16	16	1.14	2.62
coral polyp · oil and dispersant treatment	16	13	0.62	1.62
coral polyp · oil treatment	16	13	1.10	2.99
coral polyp · dispersant treatment	16	13	1.10	4.72
Polyp	10	8	4.37	11.96

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.08
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.43
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.17
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.86
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.73
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.15
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.01
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.87
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.49
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.95
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.50
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.05
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.95
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.05
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.82
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.60
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.49
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.76
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.53
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.21
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.22
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.21
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.12
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.31
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.23
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.78
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.32
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.60
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.72
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.44
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.04
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.77
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.62
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.33
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.23
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.43
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.40
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.35
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.08
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.04
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.03
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.71
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.66
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.60
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.55
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.47
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.35
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.62
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.27
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.17
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.91
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.84
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.82
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.76
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.65
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.61
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.48
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.44
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.10
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.99
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.75
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.66
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.64
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.59
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.51
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.18
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.05
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.03
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.83
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.53
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.26
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.72
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.27
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.03
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.74
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.35
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.23
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.97
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.89
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.32
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.23
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.96
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.76
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.51
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.28
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.81
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.99
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.39
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.