Gene detail

Detailed information of OS493_028839-T1 in Lophelia pertusa

Genomic Location: scaffold_169:706017...707426
NR annotation: KAJ7389870.1, Putative malate dehydrogenase 1B [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
Q8T773	Putative malate dehydrogenase 1B OS=Branchiostoma floridae OX=7739 GN=MDH1B PE=3 SV=1
Q5F204	Putative malate dehydrogenase 1B OS=Mus musculus OX=10090 GN=Mdh1b PE=2 SV=1
Q5I0G3	Putative malate dehydrogenase 1B OS=Homo sapiens OX=9606 GN=MDH1B PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009038 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02866 all species →	Ldh_1_C	lactate/malate dehydrogenase, alpha/beta C-terminal domain	Domain	Interproscan
PF00056 all species →	Ldh_1_N	lactate/malate dehydrogenase, NAD binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR010945 all species →	Family	Malate dehydrogenase, type 2	Interproscan
IPR022383 all species →	Domain	Lactate/malate dehydrogenase, C-terminal	Interproscan
IPR015955 all species →	Homologous_superfamily	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Interproscan
IPR001236 all species →	Domain	Lactate/malate dehydrogenase, N-terminal	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23382 all species →	MALATE DEHYDROGENASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006099 all species →	Biological Process	tricarboxylic acid cycle	Interproscan
GO:0006107 all species →	Biological Process	oxaloacetate metabolic process	Interproscan
GO:0006108 all species →	Biological Process	malate metabolic process	Interproscan
GO:0006734 all species →	Biological Process	NADH metabolic process	Interproscan
GO:0016615 all species →	Molecular Function	malate dehydrogenase activity	Interproscan
GO:0030060 all species →	Molecular Function	L-malate dehydrogenase (NAD+) activity	Interproscan
GO:0016616 all species →	Molecular Function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase 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_028839-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_028839-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

51.3Max TPM

7.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.79	7.45
polyp at pH7 6	18	18	3.51	6.81
coral polyp · control treatment	16	16	11.63	51.33
coral polyp · oil and dispersant treatment	16	16	9.31	43.70
coral polyp · oil treatment	16	16	7.81	13.61
coral polyp · dispersant treatment	16	16	7.12	15.00
Polyp	10	10	6.45	9.55

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.45
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.16
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.68
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.38
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.23
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.13
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.94
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.82
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.73
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.49
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.43
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.27
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.07
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.84
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.84
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.78
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.18
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.81
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.52
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.47
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.38
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.28
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.02
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.99
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.66
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.63
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.17
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.01
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.92
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.56
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.42
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.17
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.13
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.69
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.33
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.77
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.42
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.70
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.02
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.44
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.94
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.18
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.57
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.60
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.42
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.05
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.71
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.64
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.22
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.70
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.80
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.20
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.48
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.78
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.71
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.82
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.84
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.71
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.18
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.86
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.79
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.74
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.28
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.61
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.94
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.83
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.87
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.00
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.09
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.04
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.47
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.11
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.93
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.84
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.51
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.28
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.03
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.10
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.59
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.12
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.44
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.01
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.10
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.96
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.94
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.20
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.57
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.38
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.63
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.58
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.75
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.26
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.55
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.46
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.55
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.83
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.81
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.49
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.18
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.94
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.51
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.18

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.