Detailed information of g16841.t1 in Montipora capitata

Genomic Location: Sc0000725:85237...101942
NR annotation: XP_029195924.1, splicing factor 3A subunit 3-like [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
Q9D554Splicing factor 3A subunit 3 OS=Mus musculus OX=10090 GN=Sf3a3 PE=1 SV=2
Q12874Splicing factor 3A subunit 3 OS=Homo sapiens OX=9606 GN=SF3A3 PE=1 SV=1
O46106Splicing factor 3A subunit 3 OS=Drosophila melanogaster OX=7227 GN=noi PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005784 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF11931
all species →		SF3a60_Prp9_CSF3a60/Prp9 C-terminalFamilyInterproscan
PF16837
all species →		SF3A3Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9DomainInterproscan
PF12108
all species →		SF3a60_bindingdSplicing factor SF3a60 binding domainDomainInterproscan
PF13297
all species →		SDE2_2CReplication stress response SDE2 C-terminalDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR051421
all species →		FamilyRNA Processing and DNA Damage Response RegulatorInterproscan
IPR024598
all species →		DomainSplicing factor SF3a60 /Prp9 subunit, C-terminalInterproscan
IPR000690
all species →		DomainMatrin/U1-C, C2H2-type zinc fingerInterproscan
IPR031774
all species →		DomainSF3A3 domainInterproscan
IPR021966
all species →		DomainSplicing factor SF3a60 binding domainInterproscan
IPR025086
all species →		DomainSDE2-like, C-terminal domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12786
all species →		SPLICING FACTOR SF3A-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000398
all species →		Biological ProcessmRNA splicing, via spliceosomeInterproscan
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0005681
all species →		Cellular Componentspliceosomal complexInterproscan
GO:0003676
all species →		Molecular Functionnucleic acid bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0008270
all species →		Molecular Functionzinc ion bindingInterproscan

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
K12827SF3A3, SAP61, PRP9; splicing factor 3A subunit 3-Spliceosomeko03041deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g16841.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
1,713.6Max TPM
811.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 778.83 1,558.99
whole organisms · low pH treatment 15 15 831.47 1,643.24
whole organisms · extra low pH treatment pH treatment 12 12 844.28 1,713.62

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 1,558.99
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 1,549.70
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 1,369.42
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 1,358.55
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 1,305.41
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 1,241.13
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 1,182.98
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 963.53
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 636.58
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 627.63
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 611.13
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 586.69
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 571.83
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 571.58
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 548.05
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 535.54
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 309.56
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 296.11
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 191.81
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 184.50
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 154.76
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 1,643.24
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 1,588.95
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 1,526.36
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 1,509.57
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 1,217.33
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 1,131.39
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 625.99
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 588.18
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 547.92
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 547.13
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 537.78
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 483.32
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 186.41
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 185.44
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 153.01
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 1,713.62
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 1,592.40
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 1,433.47
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 1,370.35
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 1,220.24
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 614.14
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 580.38
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 550.75
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 540.32
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 175.44
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 173.64
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 166.58

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 correlated32g11915.t10.977206820426395
Negatively correlated95g8767.t1-0.957432771082277

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 →
TOP