Gene detail

Detailed information of OS493_040176-T1 in Lophelia pertusa

Genomic Location: scaffold_1828:2455...8492
NR annotation: KAJ7369268.1, hypothetical protein OS493_040176, partial [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
P21953	2-oxoisovalerate dehydrogenase subunit beta, mitochondrial OS=Homo sapiens OX=9606 GN=BCKDHB PE=1 SV=2
Q6P3A8	2-oxoisovalerate dehydrogenase subunit beta, mitochondrial OS=Mus musculus OX=10090 GN=Bckdhb PE=1 SV=2
P35738	2-oxoisovalerate dehydrogenase subunit beta, mitochondrial OS=Rattus norvegicus OX=10116 GN=Bckdhb PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004764 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02779 all species →	Transket_pyr	Transketolase, pyrimidine binding domain	Domain	Interproscan
PF02780 all species →	Transketolase_C	Transketolase, C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009014 all species →	Homologous_superfamily	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Interproscan
IPR005475 all species →	Domain	Transketolase-like, pyrimidine-binding domain	Interproscan
IPR033248 all species →	Domain	Transketolase, C-terminal domain	Interproscan
IPR029061 all species →	Homologous_superfamily	Thiamin diphosphate-binding fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR42980 all species →	2-OXOISOVALERATE DEHYDROGENASE SUBUNIT BETA-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005947 all species →	Cellular Component	obsolete mitochondrial alpha-ketoglutarate dehydrogenase complex	Interproscan
GO:0007584 all species →	Biological Process	response to nutrient	Interproscan
GO:0009083 all species →	Biological Process	branched-chain amino acid catabolic process	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K00167	BCKDHB, bkdA2; 2-oxoisovalerate dehydrogenase E1 component subunit beta	EC:1.2.4.4	Lipoic acid metabolism	ko00785	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_040176-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

12.3Max TPM

5.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	6.62	11.22
polyp at pH7 6	18	17	5.67	11.77
coral polyp · control treatment	16	16	5.61	11.60
coral polyp · oil and dispersant treatment	16	16	4.22	11.09
coral polyp · oil treatment	16	16	4.92	9.69
coral polyp · dispersant treatment	16	15	4.82	8.19
Polyp	10	10	5.62	12.27

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	-	11.22
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.76
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.45
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.44
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.48
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.88
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.87
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.43
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.37
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.94
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.42
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.44
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.62
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.40
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.77
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.45
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.26
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.85
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.85
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.75
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.47
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.30
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.07
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.49
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.19
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.15
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.85
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.16
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.28
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.06
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.60
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.70
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.01
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.90
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.61
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.61
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.05
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.99
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.46
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.36
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.94
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.73
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.95
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.89
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.66
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.09
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.76
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.39
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.35
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.98
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.94
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.91
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.77
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.69
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.47
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.12
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.92
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.70
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.47
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.16
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.69
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.50
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.99
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.66
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.81
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.54
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.01
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.79
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.24
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.19
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.18
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.18
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.59
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.54
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.48
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.25
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.19
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.69
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.67
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.80
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.44
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.36
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.99
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.95
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.52
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.00
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.80
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.31
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.21
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.65
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.27
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.68
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.95
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.91
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.67
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.54
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.48
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.26
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.03

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.