Gene detail

Detailed information of ENSBQFP00000038832.1 in Heliopora coerulea

Genomic Location: JASJOG010000159.1:81872...95465
NR annotation: XP_028396075.1, malate dehydrogenase, cytoplasmic-like [Dendronephthya gigantea]
Species Heliopora coerulea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5ZME2	Malate dehydrogenase, cytoplasmic OS=Gallus gallus OX=9031 GN=MDH1 PE=2 SV=1
Q3T145	Malate dehydrogenase, cytoplasmic OS=Bos taurus OX=9913 GN=MDH1 PE=2 SV=3
P11708	Malate dehydrogenase, cytoplasmic OS=Sus scrofa OX=9823 GN=MDH1 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004850 (this species only) · gene tree & orthology

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
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan
IPR001557 all species →	Family	L-lactate/malate dehydrogenase	Interproscan
IPR015955 all species →	Homologous_superfamily	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Interproscan
IPR010945 all species →	Family	Malate dehydrogenase, type 2	Interproscan
IPR001252 all species →	Active_site	Malate dehydrogenase, active site	Interproscan
IPR022383 all species →	Domain	Lactate/malate dehydrogenase, C-terminal	Interproscan
IPR011274 all species →	Family	Malate dehydrogenase, NAD-dependent, cytosolic	Interproscan
IPR001236 all species →	Domain	Lactate/malate dehydrogenase, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23382 all species →	MALATE DEHYDROGENASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016616 all species →	Molecular Function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Interproscan
GO:0019752 all species →	Biological Process	carboxylic acid metabolic process	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
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: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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K00025	MDH1; malate dehydrogenase	EC:1.1.1.37	Proximal tubule bicarbonate reclamation	ko04964	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000038832.1 across 37 RNA-seq samples of Heliopora coerulea. 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.

37Samples

37TPM > 0

6Conditions

1,420.5Max TPM

439.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	17	194.63	313.55
polyp and skeleton · 31C, 3week	6	6	556.34	1,258.47
polyp and skeleton · 28C, 3week	6	6	656.10	890.48
polyp and skeleton · 26C, 3week	4	4	470.29	488.79
polyp and skeleton · 28C, 24hr	2	2	691.22	777.31
polyp and skeleton · 31C, 24hr	2	2	1,200.24	1,420.50

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	313.55
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	276.75
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	254.34
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	254.21
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	224.63
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	220.91
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	209.85
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	199.59
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	181.98
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	178.08
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	168.91
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	163.98
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	161.44
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	141.92
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	131.25
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	122.38
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	104.89
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	1,258.47
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	571.34
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	415.83
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	381.29
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	377.78
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	333.35
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	890.48
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	802.50
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	612.53
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	589.15
SRR12578067	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	527.92
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	514.04
SRR12587801	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	488.79
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	465.86
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	465.82
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	460.70
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	777.31
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	605.13
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	1,420.50
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	979.97

Source: CnidoSite RNA-seq expression matrices (HCOER_TPM, StringTie quantification over 37 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.

Co-expression network

Genes whose expression across the transcriptome samples of Heliopora coerulea tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	23	ENSBQFP00000023423	0.87086744313726
Negatively correlated	13	ENSBQFP00000005560	-0.756250015452483

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list. Partner counts were matched on ENSBQFP00000038832, the spelling this network uses.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Heliopora coerulea, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →