Detailed information of XP_068695650.1 in Montipora foliosa

Genomic Location: chr2:54945828...54953246
NR annotation: XP_015775633.1, PREDICTED: DNA repair protein SWI5 homolog isoform X5 [Acropora digitifera]
Species Montipora foliosa · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
C3KJF2DNA repair protein SWI5 homolog OS=Anoplopoma fimbria OX=229290 GN=swi5 PE=2 SV=1
Q1ZZU3DNA repair protein SWI5 homolog OS=Homo sapiens OX=9606 GN=SWI5 PE=1 SV=1
A9UL70DNA repair protein SWI5 homolog OS=Xenopus tropicalis OX=8364 GN=swi5 PE=3 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007584 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF07061
all species →		Swi5Swi5FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR010760
all species →		FamilyDNA repair protein, Swi5Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR28529
all species →		DNA REPAIR PROTEIN SWI5 HOMOLOGInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000724
all species →		Biological Processdouble-strand break repair via homologous recombinationInterproscan
GO:0032798
all species →		Cellular ComponentSwi5-Sfr1 complexInterproscan
GO:0034974
all species →		Cellular ComponentSwi5-Swi2 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
K10991SWI5, SAE3; DNA repair protein Swi5/Sae3-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_068695650.1 across 36 RNA-seq samples of Montipora foliosa. 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
27TPM > 0
1Conditions
8.5Max TPM
3.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Polyps 36 27 3.48 8.47

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR12959185 Polyps Polyps E4 day21 not recorded SRP199550 8.47
SRR12959237 Polyps Polyps E4 day0 not recorded SRP199550 7.95
SRR12959225 Polyps Polyps E4 day3 not recorded SRP199550 7.50
SRR12959187 Polyps Polyps E4 day21 not recorded SRP199550 7.03
SRR12959213 Polyps Polyps E4 day9 not recorded SRP199550 6.28
SRR12959198 Polyps Polyps E4 day15 not recorded SRP199550 5.89
SRR12959199 Polyps Polyps E4 day15 not recorded SRP199550 5.67
SRR12710866 Polyps Polyps OA4 day3 not recorded SRP199550 5.27
SRR12786895 Polyps Polyps OA4 day0 not recorded SRP199550 5.21
SRR12904780 Polyps Polyps not recorded not recorded SRP199550 5.18
SRR27940180 Polyps Polyps not recorded not recorded SRP199550 5.12
SRR12959238 Polyps Polyps E4 day0 not recorded SRP199550 4.99
SRR12959181 Polyps Polyps E4 day0 not recorded SRP199550 4.90
SRR12959200 Polyps Polyps E4 day15 not recorded SRP199550 4.86
SRR12904791 Polyps Polyps not recorded not recorded SRP199550 4.70
SRR27940177 Polyps Polyps not recorded not recorded SRP199550 4.61
SRR12959224 Polyps Polyps E4 day3 not recorded SRP199550 4.44
SRR12904792 Polyps Polyps not recorded not recorded SRP199550 3.73
SRR27940179 Polyps Polyps not recorded not recorded SRP199550 3.71
SRR12959186 Polyps Polyps E4 day21 not recorded SRP199550 3.37
SRR12710865 Polyps Polyps OA4 day3 not recorded SRP199550 3.25
SRR12959211 Polyps Polyps E4 day9 not recorded SRP199550 3.04
SRR12959226 Polyps Polyps E4 day3 not recorded SRP199550 2.80
SRR12959212 Polyps Polyps E4 day9 not recorded SRP199550 2.72
SRR12786904 Polyps Polyps OA4 day0 not recorded SRP199550 2.36
SRR12710852 Polyps Polyps OA4 day9 not recorded SRP199550 1.66
SRR12710853 Polyps Polyps OA4 day9 not recorded SRP199550 0.51
SRR12710845 Polyps Polyps OA4 day3 not recorded SRP199550 0.00
SRR12710854 Polyps Polyps OA4 day9 not recorded SRP199550 0.00
SRR12786903 Polyps Polyps OA4 day0 not recorded SRP199550 0.00
SRR12807380 Polyps Polyps OA4 day0 not recorded SRP199550 0.00
SRR12849112 Polyps Polyps OA4 day0 not recorded SRP199550 0.00
SRR12927879 Polyps Polyps E4 day0 not recorded SRP199550 0.00
SRR12963483 Polyps Polyps E4 day0 not recorded SRP199550 0.00
SRR9129315 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9613518 Polyps Polyps not recorded not recorded SRP199550 0.00

Source: CnidoSite RNA-seq expression matrices (MFOLI_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 foliosa 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 correlated11XP_068710271.10.870656590234257
Negatively correlated3XP_068686099.1-0.375465646587178

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 foliosa, 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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