Detailed information of amur_s0133.g50.t1 in Acropora muricata

Genomic Location: sc0000133_pilon:597099...624925
NR annotation: XP_029207367.2, DNA-directed RNA polymerase I subunit RPA2-like [Acropora millepora]
Species Acropora muricata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
B8JKD7DNA-directed RNA polymerase I subunit RPA2 OS=Danio rerio OX=7955 GN=polr1b PE=3 SV=1
Q9H9Y6DNA-directed RNA polymerase I subunit RPA2 OS=Homo sapiens OX=9606 GN=POLR1B PE=1 SV=2
Q5REE8DNA-directed RNA polymerase I subunit RPA2 OS=Pongo abelii OX=9601 GN=POLR1B PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003184 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF04565
all species →		RNA_pol_Rpb2_3RNA polymerase Rpb2, domain 3DomainInterproscan
PF04563
all species →		RNA_pol_Rpb2_1RNA polymerase beta subunitFamilyInterproscan
PF04560
all species →		RNA_pol_Rpb2_7RNA polymerase Rpb2, domain 7DomainInterproscan
PF04561
all species →		RNA_pol_Rpb2_2RNA polymerase Rpb2, domain 2DomainInterproscan
PF00562
all species →		RNA_pol_Rpb2_6RNA polymerase Rpb2, domain 6DomainInterproscan
PF06883
all species →		RNA_pol_Rpa2_4RNA polymerase I, Rpa2 specific domain DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR037033
all species →		Homologous_superfamilyDNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyInterproscan
IPR007645
all species →		DomainRNA polymerase Rpb2, domain 3Interproscan
IPR007644
all species →		DomainRNA polymerase, beta subunit, protrusionInterproscan
IPR007641
all species →		DomainRNA polymerase Rpb2, domain 7Interproscan
IPR014724
all species →		Homologous_superfamilyRNA polymerase Rpb2, OB-foldInterproscan
IPR007121
all species →		Conserved_siteRNA polymerase, beta subunit, conserved siteInterproscan
IPR037034
all species →		Homologous_superfamilyRNA polymerase Rpb2, domain 2 superfamilyInterproscan
IPR007642
all species →		DomainRNA polymerase Rpb2, domain 2Interproscan
IPR015712
all species →		FamilyDNA-directed RNA polymerase, subunit 2Interproscan
IPR007120
all species →		DomainDNA-directed RNA polymerase, subunit 2, hybrid-binding domainInterproscan
IPR009674
all species →		DomainDNA-directed RNA polymerase I subunit RPA2, domain 4Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR20856
all species →		DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0003899
all species →		Molecular FunctionDNA-directed 5'-3' RNA polymerase activityInterproscan
GO:0006351
all species →		Biological ProcessDNA-templated transcriptionInterproscan
GO:0032549
all species →		Molecular Functionribonucleoside bindingInterproscan
GO:0001054
all species →		Molecular FunctionRNA polymerase I activityInterproscan
GO:0005736
all species →		Cellular ComponentRNA polymerase I complexInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan

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
K03002RPA2, POLR1B; DNA-directed RNA polymerase I subunit RPA2EC:2.7.7.6
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 amur_s0133.g50.t1 across 82 RNA-seq samples of Acropora muricata. 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.

82Samples
58TPM > 0
2Conditions
45.0Max TPM
5.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Polyps 79 58 5.93 44.98
Severed branch 3 0 0.00 0.00

Per sample · hover a bar for the full sample record

Show the sample table (82 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR27940226 Polyps Polyps not recorded not recorded SRP199550 44.98
SRR27868181 Polyps Polyps regeneration day33 not recorded SRP199550 34.85
SRR27868184 Polyps Polyps regeneration day30 not recorded SRP199550 23.22
SRR27868186 Polyps Polyps regeneration day30 not recorded SRP199550 18.85
SRR27868160 Polyps Polyps regeneration day6 not recorded SRP199550 16.01
SRR27868193 Polyps Polyps regeneration day24 not recorded SRP199550 15.01
SRR27868178 Polyps Polyps regeneration day36 not recorded SRP199550 12.94
SRR27868206 Polyps Polyps regeneration day12 not recorded SRP199550 12.53
SRR27868165 Polyps Polyps regeneration day3 not recorded SRP199550 11.55
SRR27868204 Polyps Polyps regeneration day12 not recorded SRP199550 10.89
SRR27868189 Polyps Polyps regeneration day27 not recorded SRP199550 8.72
SRR27868203 Polyps Polyps regeneration day15 not recorded SRP199550 8.68
SRR27868194 Polyps Polyps regeneration day21 not recorded SRP199550 8.39
SRR12959204 Polyps Polyps E2 day15 not recorded SRP199550 8.05
SRR12959217 Polyps Polyps E2 day0 not recorded SRP199550 7.87
SRR27868188 Polyps Polyps regeneration day27 not recorded SRP199550 7.81
SRR27868176 Polyps Polyps regeneration day3 not recorded SRP199550 7.78
SRR27868158 Polyps Polyps regeneration day6 not recorded SRP199550 7.65
SRR27868179 Polyps Polyps regeneration day36 not recorded SRP199550 7.48
SRR27868197 Polyps Polyps regeneration day18 not recorded SRP199550 7.45
SRR27940224 Polyps Polyps not recorded not recorded SRP199550 7.32
SRR12904784 Polyps Polyps not recorded not recorded SRP199550 7.17
SRR12959195 Polyps Polyps E2 day0 not recorded SRP199550 7.14
SRR12959219 Polyps Polyps E2 day9 not recorded SRP199550 7.09
SRR27868174 Polyps Polyps regeneration day39 not recorded SRP199550 7.07
SRR27868207 Polyps Polyps regeneration day9 not recorded SRP199550 7.03
SRR27868209 Polyps Polyps regeneration day0 not recorded SRP199550 6.87
SRR27868202 Polyps Polyps regeneration day15 not recorded SRP199550 6.85
SRR12904785 Polyps Polyps not recorded not recorded SRP199550 6.71
SRR12959191 Polyps polyps E2 day21 not recorded SRP199550 6.60
SRR12959220 Polyps Polyps E2 day9 not recorded SRP199550 6.54
SRR27868177 Polyps Polyps regeneration day39 not recorded SRP199550 6.40
SRR27868200 Polyps Polyps regeneration day18 not recorded SRP199550 6.11
SRR27940227 Polyps Polyps not recorded not recorded SRP199550 6.06
SRR12959218 Polyps Polyps E2 day9 not recorded SRP199550 5.95
SRR27868208 Polyps Polyps regeneration day9 not recorded SRP199550 5.68
SRR27868180 Polyps Polyps regeneration day36 not recorded SRP199550 5.51
SRR12959192 Polyps Polyps E2 day21 not recorded SRP199550 5.41
SRR12786900 Polyps Polyps OA 2 day0 not recorded SRP199550 5.40
SRR12786901 Polyps Polyps OA 2 day0 not recorded SRP199550 5.34
SRR12959231 Polyps Polyps E2 day3 not recorded SRP199550 5.12
SRR12786899 Polyps Polyps OA 2 day0 not recorded SRP199550 5.02
SRR12959193 Polyps Polyps E2 day21 not recorded SRP199550 5.02
SRR12959205 Polyps Polyps E2 day15 not recorded SRP199550 4.69
SRR12959233 Polyps Polyps E2 day3 not recorded SRP199550 4.60
SRR27868198 Polyps Polyps regeneration day0 not recorded SRP199550 3.75
SRR27868195 Polyps Polyps regeneration day21 not recorded SRP199550 3.51
SRR27868210 Polyps Polyps regeneration day0 not recorded SRP199550 3.40
SRR27940228 Polyps Polyps not recorded not recorded SRP199550 3.40
SRR27868196 Polyps Polyps regeneration day21 not recorded SRP199550 3.36
SRR12904786 Polyps Polyps not recorded not recorded SRP199550 3.35
SRR27940222 Polyps Polyps not recorded not recorded SRP199550 2.43
SRR12710860 Polyps Polyps OA 2 day9 not recorded SRP199550 2.42
SRR12710851 Polyps Polyps OA 2 day3 not recorded SRP199550 2.23
SRR12710849 Polyps Polyps OA 2 day3 not recorded SRP199550 1.93
SRR12710859 Polyps Polyps OA 2 day9 not recorded SRP199550 1.88
SRR12710850 Polyps Polyps OA 2 day3 not recorded SRP199550 1.69
SRR12710861 Polyps Polyps OA 2 day9 not recorded SRP199550 1.53
SRR12807382 Polyps Polyps OA2 day0 not recorded SRP199550 0.00
SRR12927881 Polyps Polyps E2 day0 not recorded SRP199550 0.00
SRR12959206 Polyps Polyps E2 day0 not recorded SRP199550 0.00
SRR12959207 Polyps Polyps E2 day15 not recorded SRP199550 0.00
SRR12959232 Polyps Polyps E2 day3 not recorded SRP199550 0.00
SRR27868159 Polyps Polyps regeneration day6 not recorded SRP199550 0.00
SRR27868175 Polyps Polyps regeneration day39 not recorded SRP199550 0.00
SRR27868182 Polyps Polyps regeneration day33 not recorded SRP199550 0.00
SRR27868183 Polyps Polyps regeneration day33 not recorded SRP199550 0.00
SRR27868185 Polyps Polyps regeneration day30 not recorded SRP199550 0.00
SRR27868187 Polyps Polyps regeneration day3 not recorded SRP199550 0.00
SRR27868190 Polyps Polyps regeneration day27 not recorded SRP199550 0.00
SRR27868191 Polyps Polyps regeneration day24 not recorded SRP199550 0.00
SRR27868192 Polyps Polyps regeneration day24 not recorded SRP199550 0.00
SRR27868199 Polyps Polyps regeneration day18 not recorded SRP199550 0.00
SRR27868201 Polyps Polyps regeneration day15 not recorded SRP199550 0.00
SRR27868205 Polyps Polyps regeneration day12 not recorded SRP199550 0.00
SRR27940225 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR27940229 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9613488 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9613516 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR12995717 Severed branch Severed branch regeneration day0 not recorded SRP199550 0.00
SRR12996627 Severed branch Severed branch regeneration day0 not recorded SRP199550 0.00
SRR12996628 Severed branch Severed branch regeneration High gene expression not recorded SRP199550 0.00

Source: CnidoSite RNA-seq expression matrices (AMURI_TPM, StringTie quantification over 82 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 muricata 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 correlated16amur_s0560.g2.t10.789317058397225
Negatively correlated18amur_s1982.g1.t1-0.235669690866754

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 muricata, 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.

DatasetTissue / stageCellsCell typesThis geneMarker of
AMURI_regenPolyps · regeneration8,72128unmapped–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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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