Detailed information of g8776.t1 in Montipora capitata

Genomic Location: Sc0000219:237678...264757
NR annotation: XP_044164794.1, cohesin subunit SA-2-like isoform X1 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q8WVM7Cohesin subunit SA-1 OS=Homo sapiens OX=9606 GN=STAG1 PE=1 SV=3
Q9D3E6Cohesin subunit SA-1 OS=Mus musculus OX=10090 GN=Stag1 PE=1 SV=3
Q9DGN1Cohesin subunit SA-1 OS=Xenopus laevis OX=8355 GN=stag1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002975 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF21581
all species →		SCDStromalin conservative domainRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR039662
all species →		FamilyCohesin subunit Scc3/SAInterproscan
IPR016024
all species →		Homologous_superfamilyArmadillo-type foldInterproscan
IPR020839
all species →		DomainStromalin conservative domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11199
all species →		STROMAL ANTIGENInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000785
all species →		Cellular ComponentchromatinInterproscan
GO:0003682
all species →		Molecular Functionchromatin bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0007062
all species →		Biological Processsister chromatid cohesionInterproscan
GO:0008278
all species →		Cellular Componentcohesin complexInterproscan

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
K06671STAG1_2, SCC3, IRR1; cohesin complex subunit SA-1/2-Chromosome and associated proteinsko03036deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g8776.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples
48TPM > 0
3Conditions
442.1Max TPM
249.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 247.15 442.06
whole organisms · low pH treatment 15 15 247.14 399.74
whole organisms · extra low pH treatment pH treatment 12 12 254.40 436.09

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 442.06
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 434.72
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 433.93
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 389.63
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 375.51
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 365.24
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 324.09
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 312.35
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 305.36
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 286.10
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 280.65
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 245.38
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 209.88
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 200.36
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 127.97
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 121.07
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 95.74
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 74.62
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 61.32
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 52.99
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 51.21
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 399.74
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 379.37
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 376.82
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 340.62
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 309.34
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 301.65
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 279.54
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 275.65
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 270.72
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 215.57
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 207.84
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 188.29
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 57.63
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 53.59
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 50.77
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 436.09
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 397.99
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 350.90
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 334.49
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 330.89
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 304.57
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 292.12
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 228.36
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 213.86
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 57.71
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 54.38
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 51.49

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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 capitata 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 correlated31g32337.t10.965356838618739
Negatively correlated39g1428.t1-0.944139380891352

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 capitata, 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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