Detailed information of asel_s0001.g120.t1 in Acropora selago

Genomic Location: sc0000001_pilon:1442893...1453062
NR annotation: XP_029188553.2, alkaline ceramidase 3-like isoform X1 [Acropora millepora]
Species Acropora selago · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9D099Alkaline ceramidase 3 OS=Mus musculus OX=10090 GN=Acer3 PE=1 SV=1
Q9NUN7Alkaline ceramidase 3 OS=Homo sapiens OX=9606 GN=ACER3 PE=1 SV=3
Q02896Alkaline ceramidase YDC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=YDC1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005673 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF05875
all species →		CeramidaseCeramidaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR008901
all species →		FamilyAlkaline ceramidaseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR46187
all species →		ALKALINE CERAMIDASE 3Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006672
all species →		Biological Processceramide metabolic processInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0016811
all species →		Molecular Functionhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidesInterproscan
GO:0030176
all species →		Cellular Componentobsolete integral component of endoplasmic reticulum membraneInterproscan
GO:0070774
all species →		Molecular Functionobsolete phytoceramidase activityInterproscan
GO:0071602
all species →		Biological Processphytosphingosine biosynthetic processInterproscan

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
K04711ACER3, YDC1; dihydroceramidaseEC:3.5.1.-
Sphingolipid metabolismko00600deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of asel_s0001.g120.t1 across 24 RNA-seq samples of Acropora selago. 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.

24Samples
19TPM > 0
1Conditions
3.1Max TPM
1.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
coral larvae 24 19 1.36 3.12

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR14308015 coral larvae coral larvae not recorded not recorded SRP315987 3.12
SRR14308011 coral larvae coral larvae not recorded not recorded SRP315987 2.77
SRR14308019 coral larvae coral larvae not recorded not recorded SRP315987 2.61
SRR14308004 coral larvae coral larvae not recorded not recorded SRP315987 2.55
SRR14308027 coral larvae coral larvae not recorded not recorded SRP315987 2.38
SRR14308006 coral larvae coral larvae not recorded not recorded SRP315987 2.36
SRR14308017 coral larvae coral larvae not recorded not recorded SRP315987 1.89
SRR14308014 coral larvae coral larvae not recorded not recorded SRP315987 1.78
SRR14308022 coral larvae coral larvae not recorded not recorded SRP315987 1.72
SRR14308021 coral larvae coral larvae not recorded not recorded SRP315987 1.69
SRR14308025 coral larvae coral larvae not recorded not recorded SRP315987 1.62
SRR14308026 coral larvae coral larvae not recorded not recorded SRP315987 1.42
SRR14308024 coral larvae coral larvae not recorded not recorded SRP315987 1.35
SRR14308010 coral larvae coral larvae not recorded not recorded SRP315987 1.18
SRR14308023 coral larvae coral larvae not recorded not recorded SRP315987 1.07
SRR14308007 coral larvae coral larvae not recorded not recorded SRP315987 1.05
SRR14308012 coral larvae coral larvae not recorded not recorded SRP315987 0.76
SRR14308020 coral larvae coral larvae not recorded not recorded SRP315987 0.76
SRR14308016 coral larvae coral larvae not recorded not recorded SRP315987 0.67
SRR14308005 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308008 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308009 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308013 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308018 coral larvae coral larvae not recorded not recorded SRP315987 0.00

Source: CnidoSite RNA-seq expression matrices (ASELA_TPM, StringTie quantification over 24 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 Acropora selago 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 correlated24asel_s0010.g80.t10.885698214980872
Negatively correlated3asel_s0082.g15.t1-0.587720928152581

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.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora selago, 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.

DNA methylation (bisulphite samples)

SampleMethylation profile
Coral_Fragment_Parentopen
Larval_Pool_Offspringopen

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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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