Detailed information of ENSBQFP00000040296.1 in Heliopora coerulea

Genomic Location: JASJOG010000175.1:451908...461309
NR annotation: CAB3977350.1, methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial [Paramuricea clavata]
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 accessionDescription
Q07536Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial OS=Bos taurus OX=9913 GN=ALDH6A1 PE=1 SV=1
Q02253Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial OS=Rattus norvegicus OX=10116 GN=Aldh6a1 PE=1 SV=1
Q9EQ20Methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial OS=Mus musculus OX=10090 GN=Aldh6a1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004065 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00171
all species →		AldedhAldehyde dehydrogenase familyFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR016163
all species →		Homologous_superfamilyAldehyde dehydrogenase, C-terminalInterproscan
IPR015590
all species →		DomainAldehyde dehydrogenase domainInterproscan
IPR010061
all species →		FamilyMethylmalonate-semialdehyde dehydrogenaseInterproscan
IPR016160
all species →		Conserved_siteAldehyde dehydrogenase, cysteine active siteInterproscan
IPR016162
all species →		Homologous_superfamilyAldehyde dehydrogenase, N-terminalInterproscan
IPR016161
all species →		Homologous_superfamilyAldehyde/histidinol dehydrogenaseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR43866
all species →		MALONATE-SEMIALDEHYDE DEHYDROGENASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0016620
all species →		Molecular Functionoxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptorInterproscan
GO:0016491
all species →		Molecular Functionoxidoreductase activityInterproscan
GO:0004491
all species →		Molecular Functionmethylmalonate-semialdehyde dehydrogenase (acylating, NAD) activityInterproscan
GO:0005739
all species →		Cellular ComponentmitochondrionInterproscan
GO:0006210
all species →		Biological Processthymine catabolic processInterproscan
GO:0006574
all species →		Biological Processvaline catabolic processInterproscan
GO:0018478
all species →		Molecular Functionmalonate-semialdehyde dehydrogenase (acetylating) activityInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K00140mmsA, iolA, ALDH6A1; malonate-semialdehyde dehydrogenase (acetylating) / methylmalonate-semialdehyde dehydrogenaseEC:1.2.1.18
EC:1.2.1.27
beta-Alanine metabolismko00410deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000040296.1 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
35TPM > 0
6Conditions
282.8Max TPM
148.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole coral 17 17 142.07 196.13
polyp and skeleton · 31C, 3week 6 6 150.70 239.66
polyp and skeleton · 28C, 3week 6 5 133.75 229.53
polyp and skeleton · 26C, 3week 4 4 193.96 282.80
polyp and skeleton · 28C, 24hr 2 2 210.11 227.91
polyp and skeleton · 31C, 24hr 2 1 92.65 185.30

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR6178770 Whole coral Whole coral not recorded not recorded ERP120267 196.13
ERR6178778 Whole coral Whole coral not recorded not recorded ERP120267 182.83
ERR6178772 Whole coral Whole coral not recorded not recorded ERP120267 167.79
ERR6178776 Whole coral Whole coral not recorded not recorded ERP120267 159.38
ERR6178774 Whole coral Whole coral not recorded not recorded ERP120267 159.06
ERR6178783 Whole coral Whole coral not recorded not recorded ERP120267 158.51
ERR6178771 Whole coral Whole coral not recorded not recorded ERP120267 156.51
ERR6178773 Whole coral Whole coral not recorded not recorded ERP120267 153.43
ERR6178781 Whole coral Whole coral not recorded not recorded ERP120267 151.74
ERR6178389 Whole coral Whole coral not recorded not recorded ERP120267 146.57
ERR6178775 Whole coral Whole coral not recorded not recorded ERP120267 141.12
ERR6178780 Whole coral Whole coral not recorded not recorded ERP120267 127.78
ERR6178388 Whole coral Whole coral not recorded not recorded ERP120267 117.03
ERR6178779 Whole coral Whole coral not recorded not recorded ERP120267 111.07
ERR6178782 Whole coral Whole coral not recorded not recorded ERP120267 100.99
ERR6178387 Whole coral Whole coral not recorded not recorded ERP120267 94.43
ERR6178777 Whole coral Whole coral not recorded not recorded ERP120267 90.82
SRR12587799 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 239.66
SRR12578065 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 178.91
SRR12587804 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 138.68
SRR12578068 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 127.49
SRR12578066 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 113.15
SRR12587800 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 106.27
SRR12587803 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 229.53
SRR12587807 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 155.42
SRR5949849 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 154.81
SRR12587808 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 141.20
SRR12587802 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 121.53
SRR12578067 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 0.00
SRR12587806 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 282.80
SRR12587801 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 200.15
SRR12587805 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 170.49
SRR12587798 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 122.39
SRR12578063 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 227.91
SRR5949850 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 192.32
SRR12578064 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 185.30
SRR5949848 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 0.00

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.

DirectionPartnersMost correlated partnerPCC
Positively correlated2ENSBQFP000000124000.731999971694146
Negatively correlated15ENSBQFP00000025975-0.731175336114889

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 ENSBQFP00000040296, 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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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