Detailed information of evm.model.Ap3.2109 in Astrangia poculata

Genomic Location: Ap3:22885688...22889173
NR annotation: XP_020606749.1, ribonucleoside-diphosphate reductase subunit M2 B-like [Orbicella faveolata]
Species Astrangia poculata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P79733Ribonucleoside-diphosphate reductase subunit M2 OS=Danio rerio OX=7955 GN=rrm2 PE=1 SV=1
P31350Ribonucleoside-diphosphate reductase subunit M2 OS=Homo sapiens OX=9606 GN=RRM2 PE=1 SV=1
Q4R7Q7Ribonucleoside-diphosphate reductase subunit M2 OS=Macaca fascicularis OX=9541 GN=RRM2 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003090 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00268
all species →		Ribonuc_red_smRibonucleotide reductase, small chainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000358
all species →		FamilyRibonucleotide reductase small subunit familyInterproscan
IPR009078
all species →		Homologous_superfamilyFerritin-like superfamilyInterproscan
IPR030475
all species →		Active_siteRibonucleotide reductase small subunit, acitve siteInterproscan
IPR033909
all species →		FamilyRibonucleotide reductase small subunitInterproscan
IPR012348
all species →		Homologous_superfamilyRibonucleotide reductase-likeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23409
all species →		RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0009263
all species →		Biological Processdeoxyribonucleotide biosynthetic processInterproscan
GO:0004748
all species →		Molecular Functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptorInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0016491
all species →		Molecular Functionoxidoreductase activityInterproscan

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
K10808RRM2; ribonucleoside-diphosphate reductase subunit M2EC:1.17.4.1
DNA repair and recombination proteinsko03400deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of evm.model.Ap3.2109 across 49 RNA-seq samples of Astrangia poculata. 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.

49Samples
0TPM > 0
4Conditions
0.0Max TPM
0.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organism · cold control 14 0 0.00 0.00
whole organism · heat control 12 0 0.00 0.00
whole organism · cold challenge 12 0 0.00 0.00
whole organism · heat challenge 11 0 0.00 0.00

Per sample · hover a bar for the full sample record

Show the sample table (49 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR10674714 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674715 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674724 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674733 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674734 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674735 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674736 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674737 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674739 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674743 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674746 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674747 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674748 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674750 whole organism · cold control whole organism not recorded cold control SRP237293 0.00
SRR10674706 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674707 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674708 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674717 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674718 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674720 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674721 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674725 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674731 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674741 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674752 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674753 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674711 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674712 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674713 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674722 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674723 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674730 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674732 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674738 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674740 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674744 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674745 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674749 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674709 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674710 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674716 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674719 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674726 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674727 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674728 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674729 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674742 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674751 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00
SRR10674754 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 0.00

Source: CnidoSite RNA-seq expression matrices (APOCU_TPM, StringTie quantification over 49 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 Astrangia poculata 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 Astrangia poculata 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 Astrangia poculata, 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.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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