Detailed information of evm.model.Ap13.2148 in Astrangia poculata

Genomic Location: Ap13:23172886...23175600
NR annotation: XP_020604208.1, uncharacterized protein LOC110043131 [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
A7S4N4Probable serine incorporator OS=Nematostella vectensis OX=45351 GN=serinc PE=3 SV=1
Q3MHV9Serine incorporator 1 OS=Bos taurus OX=9913 GN=SERINC1 PE=2 SV=1
Q9NRX5Serine incorporator 1 OS=Homo sapiens OX=9606 GN=SERINC1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000609 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03348
all species →		SerincSerine incorporator (Serinc)FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR005016
all species →		FamilySerine incorporator/TMS membrane proteinInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10383
all species →		SERINE INCORPORATORInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0016020
all species →		Cellular ComponentmembraneInterproscan

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
K23544SERINC1; serine incorporator 1-Membrane traffickingko04131deepkoala

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.Ap13.2148 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
20TPM > 0
4Conditions
806.6Max TPM
105.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organism · cold control 14 3 94.92 806.59
whole organism · heat control 12 5 124.37 629.25
whole organism · cold challenge 12 7 112.23 497.18
whole organism · heat challenge 11 5 92.16 292.68

Per sample · hover a bar for the full sample record

Show the sample table (49 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR10674724 whole organism · cold control whole organism not recorded cold control SRP237293 806.59
SRR10674714 whole organism · cold control whole organism not recorded cold control SRP237293 479.46
SRR10674750 whole organism · cold control whole organism not recorded cold control SRP237293 42.89
SRR10674715 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
SRR10674741 whole organism · heat control whole organism not recorded heat control SRP237293 629.25
SRR10674718 whole organism · heat control whole organism not recorded heat control SRP237293 296.52
SRR10674731 whole organism · heat control whole organism not recorded heat control SRP237293 278.08
SRR10674753 whole organism · heat control whole organism not recorded heat control SRP237293 145.64
SRR10674706 whole organism · heat control whole organism not recorded heat control SRP237293 142.94
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
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
SRR10674740 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 497.18
SRR10674722 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 184.42
SRR10674744 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 179.19
SRR10674712 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 128.49
SRR10674713 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 126.90
SRR10674711 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 122.95
SRR10674723 whole organism · cold challenge whole organism not recorded cold challenge SRP237293 107.69
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
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
SRR10674719 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 292.68
SRR10674710 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 194.76
SRR10674729 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 189.73
SRR10674727 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 171.09
SRR10674726 whole organism · heat challenge whole organism not recorded heat challenge SRP237293 165.48
SRR10674709 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
SRR10674728 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 correlated2evm.model.Ap2.33670.745359155357571
Negatively correlated28evm.model.Ap4.5064-0.35612837549493

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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