Detailed information of gene08470.t1 in Actinoscyphia liui

Genomic Location: chr11:9658740...9675190
NR annotation: XP_028513392.1, mutS protein homolog 4 [Exaiptasia diaphana]
Species Actinoscyphia liui · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
O15457MutS protein homolog 4 OS=Homo sapiens OX=9606 GN=MSH4 PE=1 SV=2
Q99MT2MutS protein homolog 4 OS=Mus musculus OX=10090 GN=Msh4 PE=2 SV=1
F4JP48DNA mismatch repair protein MSH4 OS=Arabidopsis thaliana OX=3702 GN=MSH4 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003274 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00488
all species →		MutS_VMutS domain VDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR027417
all species →		Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR045076
all species →		FamilyDNA mismatch repair MutS familyInterproscan
IPR000432
all species →		DomainDNA mismatch repair protein MutS, C-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11361
all species →		DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003690
all species →		Molecular Functiondouble-stranded DNA bindingInterproscan
GO:0005524
all species →		Molecular FunctionATP bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006298
all species →		Biological Processmismatch repairInterproscan
GO:0007131
all species →		Biological Processreciprocal meiotic recombinationInterproscan
GO:0030983
all species →		Molecular Functionmismatched DNA bindingInterproscan
GO:0140664
all species →		Molecular FunctionATP-dependent DNA damage sensor activityInterproscan

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
No KEGG orthology assignment for gene08470.t1.

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

Co-expression network

Genes whose expression across the transcriptome samples of Actinoscyphia liui 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Actinoscyphia liui, 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.no expression matrix–
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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