Gene detail

Detailed information of OS493_001649-T1 in Lophelia pertusa

Genomic Location: scaffold_3:7508448...7550516
NR annotation: KAJ7381501.1, D-2-hydroxyglutarate dehydrogenase, mitochondrial [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
Q1JPD3	D-2-hydroxyglutarate dehydrogenase, mitochondrial OS=Bos taurus OX=9913 GN=D2HGDH PE=2 SV=2
Q8N465	D-2-hydroxyglutarate dehydrogenase, mitochondrial OS=Homo sapiens OX=9606 GN=D2HGDH PE=1 SV=3
Q8CIM3	D-2-hydroxyglutarate dehydrogenase, mitochondrial OS=Mus musculus OX=10090 GN=D2hgdh PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004203 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01565 all species →	FAD_binding_4	FAD binding domain	Domain	Interproscan
PF02913 all species →	FAD-oxidase_C	FAD linked oxidases, C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016166 all species →	Domain	FAD-binding domain, PCMH-type	Interproscan
IPR016169 all species →	Homologous_superfamily	FAD-binding, type PCMH, subdomain 2	Interproscan
IPR036318 all species →	Homologous_superfamily	FAD-binding, type PCMH-like superfamily	Interproscan
IPR051264 all species →	Family	FAD-binding Oxidoreductase/Transferase Type 4	Interproscan
IPR006094 all species →	Domain	FAD linked oxidase, N-terminal	Interproscan
IPR004113 all species →	Domain	FAD-binding oxidoreductase/transferase, type 4, C-terminal	Interproscan
IPR016164 all species →	Homologous_superfamily	FAD-linked oxidase-like, C-terminal	Interproscan
IPR016167 all species →	Homologous_superfamily	FAD-binding, type PCMH, subdomain 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43716 all species →	D-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0071949 all species →	Molecular Function	FAD binding	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0003824 all species →	Molecular Function	catalytic 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

No KEGG orthology assignment for OS493_001649-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_001649-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

108TPM > 0

7Conditions

20.3Max TPM

7.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.06	14.82
polyp at pH7 6	18	16	8.52	19.32
coral polyp · control treatment	16	16	8.26	18.53
coral polyp · oil and dispersant treatment	16	16	5.88	10.39
coral polyp · oil treatment	16	16	8.25	12.89
coral polyp · dispersant treatment	16	16	8.85	20.27
Polyp	10	10	7.23	10.90

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.82
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.12
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.64
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.01
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.98
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.51
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.51
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.03
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.84
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.63
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.60
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.36
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.07
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.35
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.82
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.05
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.47
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.30
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.32
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.57
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.84
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.55
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.75
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.53
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.42
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.41
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.57
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.24
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.05
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.50
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.26
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.53
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.19
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.84
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.19
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.85
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.69
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.40
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.21
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.34
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.83
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.24
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.59
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.77
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.83
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.37
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.39
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.71
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.14
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.04
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.77
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.60
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.55
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.33
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.34
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.15
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.50
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.45
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.20
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.95
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.04
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.01
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.89
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.62
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.76
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.74
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.66
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.95
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.74
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.60
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.04
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.72
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.55
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.42
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.39
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.93
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.27
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.30
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.93
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.97
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.88
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.32
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.28
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.23
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.68
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.54
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.12
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.07
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.29
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.68
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.11
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.90
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.60
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.38
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.20
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	8.41
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.87
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.49
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.29
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.63
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.56

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.