Detailed information of XP_068753753.1 in Montipora capricornis

Genomic Location: chr6:8949272...8963198
NR annotation: CAH3162670.1, unnamed protein product [Porites evermanni]
Species Montipora capricornis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q5RKQ0Pre-mRNA-splicing factor SPF27 OS=Danio rerio OX=7955 GN=bcas2 PE=2 SV=1
Q6PBE2Pre-mRNA-splicing factor SPF27 OS=Xenopus tropicalis OX=8364 GN=bcas2 PE=2 SV=1
O75934Pre-mRNA-splicing factor SPF27 OS=Homo sapiens OX=9606 GN=BCAS2 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006937 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF05700
all species →		BCAS2Breast carcinoma amplified sequence 2 (BCAS2)FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR008409
all species →		FamilyPre-mRNA-splicing factor SPF27Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13296
all species →		BCAS2 PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000974
all species →		Cellular ComponentPrp19 complexInterproscan
GO:0006397
all species →		Biological ProcessmRNA processingInterproscan
GO:0071011
all species →		Cellular Componentprecatalytic spliceosomeInterproscan
GO:0071013
all species →		Cellular Componentcatalytic step 2 spliceosomeInterproscan

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
K12861BCAS2; pre-mRNA-splicing factor SPF27-DNA repair and recombination proteinsko03400deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068753753.1 across 36 RNA-seq samples of Montipora capricornis. 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.

36Samples
30TPM > 0
1Conditions
125.3Max TPM
73.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Polyps 36 30 73.47 125.35

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR12959229 Polyps Polyps E3 day3 not recorded SRP199550 125.35
SRR12710857 Polyps Polyps OA3 day9 not recorded SRP199550 111.88
SRR27940191 Polyps Polyps not recorded not recorded SRP199550 108.76
SRR12904783 Polyps Polyps not recorded not recorded SRP199550 107.95
SRR12710855 Polyps Polyps OA3 day9 not recorded SRP199550 107.43
SRR12710858 Polyps Polyps OA3 day9 not recorded SRP199550 107.20
SRR27940193 Polyps Polyps not recorded not recorded SRP199550 96.61
SRR12959201 Polyps Polyps E3 day15 not recorded SRP199550 95.93
SRR12959190 Polyps Polyps E3 day21 not recorded SRP199550 93.33
SRR12959214 Polyps Polyps E3 day9 not recorded SRP199550 89.95
SRR12959202 Polyps Polyps E3 day15 not recorded SRP199550 89.90
SRR12959203 Polyps Polyps E3 day15 not recorded SRP199550 88.29
SRR12959188 Polyps Polyps E3 day21 not recorded SRP199550 88.26
SRR12904782 Polyps Polyps not recorded not recorded SRP199550 88.12
SRR12904781 Polyps Polyps not recorded not recorded SRP199550 88.01
SRR12959184 Polyps Polyps E3 day0 not recorded SRP199550 87.93
SRR12959216 Polyps Polyps E3 day9 not recorded SRP199550 87.82
SRR12959227 Polyps Polyps E3 day3 not recorded SRP199550 86.33
SRR12959189 Polyps Polyps E3 day21 not recorded SRP199550 86.20
SRR12959215 Polyps Polyps E3 day9 not recorded SRP199550 85.81
SRR12786898 Polyps Polyps OA3 day0 not recorded SRP199550 81.86
SRR12710848 Polyps Polyps OA3 day3 not recorded SRP199550 78.85
SRR12786897 Polyps Polyps OA3 day0 not recorded SRP199550 78.02
SRR12786896 Polyps Polyps OA3 day0 not recorded SRP199550 77.98
SRR12959183 Polyps Polyps E3 day0 not recorded SRP199550 77.95
SRR12959230 Polyps Polyps E3 day3 not recorded SRP199550 75.81
SRR12710846 Polyps Polyps OA3 day3 not recorded SRP199550 73.47
SRR12959182 Polyps Polyps E3 day0 not recorded SRP199550 71.70
SRR12710847 Polyps Polyps OA3 day3 not recorded SRP199550 71.58
SRR27940192 Polyps Polyps not recorded not recorded SRP199550 36.55
SRR12807381 Polyps Polyps OA3 day0 not recorded SRP199550 0.00
SRR12849113 Polyps Polyps OA3 day0 not recorded SRP199550 0.00
SRR12927880 Polyps Polyps E3 day0 not recorded SRP199550 0.00
SRR12963484 Polyps Polyps E3 day0 not recorded SRP199550 0.00
SRR9129316 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9613519 Polyps Polyps not recorded not recorded SRP199550 0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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 capricornis 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 correlated23XP_068749241.10.93283055052286
Negatively correlated9XP_068724527.1-0.612322262521939

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 capricornis, 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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