Detailed information of BRAKERXEIP00000026459.1 in Muricea muricata

Genomic Location: chr13:1401399...1406769
NR annotation: XP_028407058.1, survival motor neuron protein 1-like [Dendronephthya gigantea]
Species Muricea muricata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9W6S8Survival motor neuron protein 1 OS=Danio rerio OX=7955 GN=smn1 PE=1 SV=1
P97801Survival motor neuron protein OS=Mus musculus OX=10090 GN=Smn1 PE=1 SV=1
O18870Survival motor neuron protein OS=Bos taurus OX=9913 GN=SMN1 PE=2 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005844 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF20636
all species →
SMN_G2-BDSurvival Motor Neuron, Gemin2-binding domainDomainInterproscan
PF20635
all species →
SMN_YG-boxSurvival Motor Neuron, YG-boxDomainInterproscan
PF06003
all species →
SMN_TudorSurvival motor neuron protein (SMN), Tudor domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR047313
all species →
DomainSurvival motor neuron protein, C-terminal oligomerization domainInterproscan
IPR040424
all species →
FamilySMN complex subunit Smn1Interproscan
IPR002999
all species →
DomainTudor domainInterproscan
IPR047298
all species →
DomainSurvival motor neuron protein, Tudor domain, eumetazoaInterproscan
IPR010304
all species →
DomainSurvival motor neuron, Tudor domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR39267
all species →
SURVIVAL MOTOR NEURON-LIKE PROTEIN 1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003723
all species →
Molecular FunctionRNA bindingInterproscan
GO:0005634
all species →
Cellular ComponentnucleusInterproscan
GO:0005737
all species →
Cellular ComponentcytoplasmInterproscan
GO:0006397
all species →
Biological ProcessmRNA processingInterproscan

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
K13129SMN; survival motor neuron protein-Spliceosomeko03041deepkoala

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 Muricea muricata 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 Muricea muricata, 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 →
TOP