Detailed information of XP_068762098.1 in Montipora capricornis

Genomic Location: chr8:15871259...15911355
NR annotation: XP_029180649.1, DNA-directed RNA polymerase III subunit RPC5-like isoform X1 [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9NVU0DNA-directed RNA polymerase III subunit RPC5 OS=Homo sapiens OX=9606 GN=POLR3E PE=1 SV=1
Q9CZT4DNA-directed RNA polymerase III subunit RPC5 OS=Mus musculus OX=10090 GN=Polr3e PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003437 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF19725
all species →		RPC5_CDNA-directed RNA polymerase III subunit RPC5 C-terminalDomainInterproscan
PF04801
all species →		RPC5RPC5 proteinFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR006886
all species →		FamilyDNA-directed RNA polymerase III subunit Rpc5Interproscan
IPR045576
all species →		DomainDNA-directed RNA polymerase III subunit RPC5, C-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12069
all species →		DNA-DIRECTED RNA POLYMERASES III 80 KDA POLYPEPTIDE RNA POLYMERASE III SUBUNIT 5Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0005666
all species →		Cellular ComponentRNA polymerase III complexInterproscan
GO:0006351
all species →		Biological ProcessDNA-templated transcriptionInterproscan
GO:0042797
all species →		Biological ProcesstRNA transcription by RNA polymerase IIIInterproscan

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
K14721RPC5, POLR3E; DNA-directed RNA polymerase III subunit RPC5-Transcription machineryko03021deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068762098.1 across 36 RNA-seq samples of Montipora capricornis. 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.

36Samples
27TPM > 0
1Conditions
28.8Max TPM
11.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Polyps 36 27 11.42 28.76

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR12904783 Polyps Polyps not recorded not recorded SRP199550 28.76
SRR27940191 Polyps Polyps not recorded not recorded SRP199550 28.57
SRR12786897 Polyps Polyps OA3 day0 not recorded SRP199550 22.73
SRR12904781 Polyps Polyps not recorded not recorded SRP199550 22.31
SRR12959229 Polyps Polyps E3 day3 not recorded SRP199550 21.72
SRR27940193 Polyps Polyps not recorded not recorded SRP199550 20.57
SRR12786896 Polyps Polyps OA3 day0 not recorded SRP199550 19.55
SRR12904782 Polyps Polyps not recorded not recorded SRP199550 19.20
SRR12786898 Polyps Polyps OA3 day0 not recorded SRP199550 19.09
SRR12959184 Polyps Polyps E3 day0 not recorded SRP199550 16.68
SRR12959182 Polyps Polyps E3 day0 not recorded SRP199550 16.28
SRR12959183 Polyps Polyps E3 day0 not recorded SRP199550 15.36
SRR12959203 Polyps Polyps E3 day15 not recorded SRP199550 14.39
SRR12959215 Polyps Polyps E3 day9 not recorded SRP199550 13.48
SRR12959214 Polyps Polyps E3 day9 not recorded SRP199550 13.47
SRR12959201 Polyps Polyps E3 day15 not recorded SRP199550 12.81
SRR12959202 Polyps Polyps E3 day15 not recorded SRP199550 12.22
SRR12959216 Polyps Polyps E3 day9 not recorded SRP199550 11.73
SRR12710858 Polyps Polyps OA3 day9 not recorded SRP199550 11.59
SRR12710848 Polyps Polyps OA3 day3 not recorded SRP199550 10.89
SRR12959189 Polyps Polyps E3 day21 not recorded SRP199550 10.10
SRR12710846 Polyps Polyps OA3 day3 not recorded SRP199550 10.08
SRR12710847 Polyps Polyps OA3 day3 not recorded SRP199550 9.20
SRR12959190 Polyps Polyps E3 day21 not recorded SRP199550 8.84
SRR12710855 Polyps Polyps OA3 day9 not recorded SRP199550 8.20
SRR12710857 Polyps Polyps OA3 day9 not recorded SRP199550 6.60
SRR12959188 Polyps Polyps E3 day21 not recorded SRP199550 6.55
SRR12807381 Polyps Polyps OA3 day0 not recorded SRP199550 0.00
SRR12849113 Polyps Polyps OA3 day0 not recorded SRP199550 0.00
SRR12927880 Polyps Polyps E3 day0 not recorded SRP199550 0.00
SRR12959227 Polyps Polyps E3 day3 not recorded SRP199550 0.00
SRR12959230 Polyps Polyps E3 day3 not recorded SRP199550 0.00
SRR12963484 Polyps Polyps E3 day0 not recorded SRP199550 0.00
SRR27940192 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9129316 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9613519 Polyps Polyps not recorded not recorded SRP199550 0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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 Montipora capricornis 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 correlated45XP_068719682.10.978008140989763
Negatively correlated3XP_068724527.1-0.402876124160641

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 Montipora capricornis, 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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