Detailed information of evm.model.Ap13.1737 in Astrangia poculata

Genomic Location: Ap13:18527777...18529048
NR annotation: KAJ7374208.1, hypothetical protein OS493_007281 [Desmophyllum pertusum]
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)
No Swiss-Prot hit above the reporting threshold for this gene.
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001297 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF14388
all species →		DUF4419Domain of unknown function (DUF4419)FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR025533
all species →		FamilyProtein of unknown function DUF4419Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR31252
all species →		-Interproscan

 Gene Ontology
No Gene Ontology signature was recorded for evm.model.Ap13.1737 in Astrangia poculata.
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
K03821phaC, phbC; poly[(R)-3-hydroxyalkanoate] polymerase subunit PhaCEC:2.3.1.304
Butanoate metabolismko00650deepkoala

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.Ap13.1737 across 49 RNA-seq samples of Astrangia poculata. 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
19TPM > 0
4Conditions
1,295.8Max TPM
182.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organism · cold control 14 5 117.26 518.91
whole organism · heat control 12 7 235.34 903.63
whole organism · cold challenge 12 6 321.67 1,295.81
whole organism · heat challenge 11 1 53.83 592.10

Per sample · hover a bar for the full sample record

Show the sample table (49 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR10674743 whole organism · cold control whole organism not recorded cold control SRP237293 518.91
SRR10674715 whole organism · cold control whole organism not recorded cold control SRP237293 349.06
SRR10674736 whole organism · cold control whole organism not recorded cold control SRP237293 317.42
SRR10674735 whole organism · cold control whole organism not recorded cold control SRP237293 264.42
SRR10674750 whole organism · cold control whole organism not recorded cold control SRP237293 191.82
SRR10674714 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
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
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
SRR10674708 whole organism · heat control whole organism not recorded heat control SRP237293 903.63
SRR10674718 whole organism · heat control whole organism not recorded heat control SRP237293 586.25
SRR10674741 whole organism · heat control whole organism not recorded heat control SRP237293 360.16
SRR10674731 whole organism · heat control whole organism not recorded heat control SRP237293 296.76
SRR10674707 whole organism · heat control whole organism not recorded heat control SRP237293 267.12
SRR10674717 whole organism · heat control whole organism not recorded heat control SRP237293 239.16
SRR10674753 whole organism · heat control whole organism not recorded heat control SRP237293 170.97
SRR10674706 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
SRR10674752 whole organism · heat control whole organism not recorded heat control SRP237293 0.00
SRR10674713 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 1,295.81
SRR10674745 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 762.12
SRR10674711 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 734.84
SRR10674712 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 623.32
SRR10674723 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 240.31
SRR10674722 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 203.60
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
SRR10674749 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 0.00
SRR10674754 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 592.10
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

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 correlated1evm.model.Ap4.7960.721201506686467
Negatively correlated26evm.model.Ap13.2084-0.380445489536349

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.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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