Detailed information of ENSSYXP00000025239.1 in Micromussa lordhowensis

Genomic Location: chr13:3370625...3371815
NR annotation: XP_029180051.1, U6 snRNA-associated Sm-like protein LSm5 [Acropora millepora]
Species Micromussa lordhowensis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q2HJH0U6 snRNA-associated Sm-like protein LSm5 OS=Bos taurus OX=9913 GN=LSM5 PE=3 SV=3
Q9Y4Y9U6 snRNA-associated Sm-like protein LSm5 OS=Homo sapiens OX=9606 GN=LSM5 PE=1 SV=3
P62322U6 snRNA-associated Sm-like protein LSm5 OS=Mus musculus OX=10090 GN=Lsm5 PE=3 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0010345 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01423
all species →		LSMLSM domain DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR033871
all species →		DomainSm-like protein LSm5Interproscan
IPR001163
all species →		DomainSm domain, eukaryotic/archaea-typeInterproscan
IPR010920
all species →		Homologous_superfamilyLSM domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR20971
all species →		U6 SNRNA-ASSOCIATED PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000398
all species →		Biological ProcessmRNA splicing, via spliceosomeInterproscan
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0005688
all species →		Cellular ComponentU6 snRNPInterproscan
GO:0046540
all species →		Cellular ComponentU4/U6 x U5 tri-snRNP complexInterproscan
GO:1990726
all species →		Cellular ComponentLsm1-7-Pat1 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
No KEGG orthology assignment for ENSSYXP00000025239.1.

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 Micromussa lordhowensis 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 Micromussa lordhowensis, 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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