Detailed information of g9871.t1 in Montipora capitata

Genomic Location: Sc0000267:4347...12256
NR annotation: XP_029212771.2, splicing factor 45-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
Q96I25Splicing factor 45 OS=Homo sapiens OX=9606 GN=RBM17 PE=1 SV=1
Q8JZX4Splicing factor 45 OS=Mus musculus OX=10090 GN=Rbm17 PE=1 SV=1
P42698DNA-damage-repair/toleration protein 111 OS=Arabidopsis thaliana OX=3702 GN=DRT111 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006394 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01585
all species →		G-patchG-patch domainFamilyInterproscan
PF00076
all species →		RRM_1RNA recognition motifDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR040052
all species →		FamilySplicing factor 45Interproscan
IPR000467
all species →		DomainG-patch domainInterproscan
IPR035979
all species →		Homologous_superfamilyRNA-binding domain superfamilyInterproscan
IPR000504
all species →		DomainRNA recognition motif domainInterproscan
IPR003954
all species →		DomainRNA recognition motif domain, eukaryoteInterproscan
IPR012677
all species →		Homologous_superfamilyNucleotide-binding alpha-beta plait domain superfamilyInterproscan
IPR034653
all species →		DomainSPF45, RNA recognition motifInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13288
all species →		SPLICING FACTOR 45 SPF45Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000380
all species →		Biological Processalternative mRNA splicing, via spliceosomeInterproscan
GO:0000398
all species →		Biological ProcessmRNA splicing, via spliceosomeInterproscan
GO:0045292
all species →		Biological ProcessmRNA cis splicing, via spliceosomeInterproscan
GO:0071011
all species →		Cellular Componentprecatalytic spliceosomeInterproscan
GO:0003676
all species →		Molecular Functionnucleic acid bindingInterproscan
GO:0003723
all species →		Molecular FunctionRNA 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
K12840RBM17, SPF45; splicing factor 45-Spliceosomeko03041deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g9871.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
47TPM > 0
3Conditions
187.1Max TPM
66.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 20 74.21 187.08
whole organisms · low pH treatment 15 15 62.09 143.79
whole organisms · extra low pH treatment pH treatment 12 12 60.19 142.63

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 187.08
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 181.50
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 152.60
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 130.05
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 127.65
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 122.98
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 92.77
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 91.28
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 85.05
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 84.82
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 82.47
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 82.14
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 80.02
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 19.58
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 12.13
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 6.05
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 6.01
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 5.04
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 4.87
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 4.25
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 0.00
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 143.79
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 138.04
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 134.60
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 81.14
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 80.13
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 78.10
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 77.70
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 75.98
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 73.13
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 15.29
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 14.61
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 9.19
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 5.09
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 3.73
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 0.77
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 142.63
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 124.67
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 92.66
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 88.00
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 83.12
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 77.92
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 77.69
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 11.69
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 10.78
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 4.79
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 4.70
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 3.60

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 correlated54g5592.t10.984975610152469
Negatively correlated32g7927.t1-0.933645865405333

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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