Detailed information of asel_s0055.g2.t1 in Acropora selago

Genomic Location: sc0000055_pilon:38352...52835
NR annotation: XP_015764005.1, PREDICTED: ribonuclease P protein subunit p29-like [Acropora digitifera]
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
Q2KIB9Ribonuclease P protein subunit p29 OS=Bos taurus OX=9913 GN=POP4 PE=2 SV=1
Q5R7B0Ribonuclease P protein subunit p29 OS=Pongo abelii OX=9601 GN=POP4 PE=2 SV=1
O95707Ribonuclease P protein subunit p29 OS=Homo sapiens OX=9606 GN=POP4 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007530 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01868
all species →		RNase_P-MRP_p29Ribonuclease P/MRP, subunit p29FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036980
all species →		Homologous_superfamilyRibonuclease P/MRP subunit Rpp29 superfamilyInterproscan
IPR023534
all species →		Homologous_superfamilyRof/RNase P-likeInterproscan
IPR002730
all species →		FamilyRibonuclease P protein subunit Rpp29/RNP1Interproscan
IPR016848
all species →		FamilyRibonuclease P/MRP subunit Rpp29Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13348
all species →		RIBONUCLEASE P SUBUNIT P29Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0008033
all species →		Biological ProcesstRNA processingInterproscan
GO:0030677
all species →		Cellular Componentribonuclease P complexInterproscan
GO:0001682
all species →		Biological ProcesstRNA 5'-leader removalInterproscan
GO:0006396
all species →		Biological ProcessRNA processingInterproscan
GO:0000172
all species →		Cellular Componentribonuclease MRP complexInterproscan
GO:0033204
all species →		Molecular Functionribonuclease P RNA bindingInterproscan
GO:0006364
all species →		Biological ProcessrRNA processingInterproscan

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
K03538POP4, RPP29; ribonuclease P protein subunit POP4EC:3.1.26.5
Mitochondrial biogenesisko03029deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of asel_s0055.g2.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
23TPM > 0
1Conditions
111.7Max TPM
44.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
coral larvae 24 23 44.39 111.68

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR14308018 coral larvae coral larvae not recorded not recorded SRP315987 111.68
SRR14308024 coral larvae coral larvae not recorded not recorded SRP315987 59.18
SRR14308009 coral larvae coral larvae not recorded not recorded SRP315987 57.66
SRR14308012 coral larvae coral larvae not recorded not recorded SRP315987 51.94
SRR14308026 coral larvae coral larvae not recorded not recorded SRP315987 49.46
SRR14308015 coral larvae coral larvae not recorded not recorded SRP315987 46.41
SRR14308017 coral larvae coral larvae not recorded not recorded SRP315987 45.96
SRR14308025 coral larvae coral larvae not recorded not recorded SRP315987 45.89
SRR14308027 coral larvae coral larvae not recorded not recorded SRP315987 45.81
SRR14308006 coral larvae coral larvae not recorded not recorded SRP315987 45.58
SRR14308011 coral larvae coral larvae not recorded not recorded SRP315987 45.07
SRR14308004 coral larvae coral larvae not recorded not recorded SRP315987 44.73
SRR14308010 coral larvae coral larvae not recorded not recorded SRP315987 44.65
SRR14308007 coral larvae coral larvae not recorded not recorded SRP315987 44.49
SRR14308021 coral larvae coral larvae not recorded not recorded SRP315987 41.30
SRR14308022 coral larvae coral larvae not recorded not recorded SRP315987 41.06
SRR14308008 coral larvae coral larvae not recorded not recorded SRP315987 39.38
SRR14308013 coral larvae coral larvae not recorded not recorded SRP315987 36.73
SRR14308019 coral larvae coral larvae not recorded not recorded SRP315987 35.93
SRR14308020 coral larvae coral larvae not recorded not recorded SRP315987 35.46
SRR14308014 coral larvae coral larvae not recorded not recorded SRP315987 33.68
SRR14308016 coral larvae coral larvae not recorded not recorded SRP315987 32.20
SRR14308023 coral larvae coral larvae not recorded not recorded SRP315987 31.22
SRR14308005 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 correlated38asel_s0016.g125.t10.936678888265722
Negatively correlated12asel_s0001.g108.t1-0.836622390718709

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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