Detailed information of asel_s0050.g4.t2 in Acropora selago

Genomic Location: sc0000050_pilon:97740...108915
NR annotation: XP_029187907.2, DNA helicase MCM9-like [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
I0IUP4DNA helicase MCM9 OS=Gallus gallus OX=9031 GN=MCM9 PE=1 SV=2
F1QDI9DNA helicase MCM9 OS=Danio rerio OX=7955 GN=mcm9 PE=3 SV=2
F6RIX4DNA helicase MCM9 OS=Xenopus tropicalis OX=8364 GN=mcm9 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004980 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00493
all species →		MCMMCM P-loop domainDomainInterproscan
PF17855
all species →		MCM_lidMCM AAA-lid domainDomainInterproscan
PF17207
all species →		MCM_OBMCM OB domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001208
all species →		DomainMCM domainInterproscan
IPR027417
all species →		Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR012340
all species →		Homologous_superfamilyNucleic acid-binding, OB-foldInterproscan
IPR003593
all species →		DomainAAA+ ATPase domainInterproscan
IPR041562
all species →		DomainMCM, AAA-lid domainInterproscan
IPR031327
all species →		FamilyMini-chromosome maintenance proteinInterproscan
IPR033762
all species →		DomainMCM OB domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11630
all species →		DNA REPLICATION LICENSING FACTOR MCM FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0005524
all species →		Molecular FunctionATP bindingInterproscan
GO:0032508
all species →		Biological ProcessDNA duplex unwindingInterproscan
GO:0016887
all species →		Molecular FunctionATP hydrolysis activityInterproscan
GO:0000724
all species →		Biological Processdouble-strand break repair via homologous recombinationInterproscan
GO:0003697
all species →		Molecular Functionsingle-stranded DNA bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0017116
all species →		Molecular Functionsingle-stranded DNA helicase activityInterproscan
GO:0042555
all species →		Cellular ComponentMCM complexInterproscan

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
K10738MCM9; DNA helicase MCM9EC:5.6.2.4
DNA replication proteinsko03032deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of asel_s0050.g4.t2 across 24 RNA-seq samples of Acropora selago. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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
0TPM > 0
1Conditions
0.0Max TPM
0.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
coral larvae 24 0 0.00 0.00

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR14308004 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308005 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308006 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308007 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
SRR14308010 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308011 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308012 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308013 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308014 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308015 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308016 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308017 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308018 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308019 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308020 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308021 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308022 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308023 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308024 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308025 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308026 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308027 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 correlated0not in this network-
Negatively correlated0not in this network-

This gene has no edge at all in the Acropora selago network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.

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.no expression matrix–
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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