Detailed information of ANN27367-RA in Montipora grisea

Genomic Location: Scaffold_669__1_contigs__length_80378:64598...65650
NR annotation: PCJ24947.1, tRNA 2-thiouridine(34) synthase MnmA [Rickettsiales bacterium]
Species Montipora grisea · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
A8EZE8tRNA-specific 2-thiouridylase MnmA OS=Rickettsia canadensis (strain McKiel) OX=293613 GN=mnmA PE=3 SV=1
Q92IL0tRNA-specific 2-thiouridylase MnmA OS=Rickettsia conorii (strain ATCC VR-613 / Malish 7) OX=272944 GN=mnmA PE=3 SV=1
C3PN11tRNA-specific 2-thiouridylase MnmA OS=Rickettsia africae (strain ESF-5) OX=347255 GN=mnmA PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0013736 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF20258
all species →
tRNA_Me_trans_CAminomethyltransferase beta-barrel domainDomainInterproscan
PF03054
all species →
tRNA_Me_transtRNA methyl transferase HUP domainDomainInterproscan
PF20259
all species →
tRNA_Me_trans_MtRNA methyl transferase PRC-barrel domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR004506
all species →
FamilytRNA-specific 2-thiouridylaseInterproscan
IPR046885
all species →
DomaintRNA-specific 2-thiouridylase MnmA-like, C-terminal domainInterproscan
IPR014729
all species →
Homologous_superfamilyRossmann-like alpha/beta/alpha sandwich foldInterproscan
IPR046884
all species →
DomaintRNA-specific 2-thiouridylase MnmA-like, central domainInterproscan
IPR023382
all species →
Homologous_superfamilytRNA-specific 2-thiouridylase MnmA-like, central domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11933
all species →
TRNA 5-METHYLAMINOMETHYL-2-THIOURIDYLATE -METHYLTRANSFERASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0008033
all species →
Biological ProcesstRNA processingInterproscan
GO:0016740
all species →
Molecular Functiontransferase activityInterproscan
GO:0002143
all species →
Biological ProcesstRNA wobble position uridine thiolationInterproscan
GO:0016783
all species →
Molecular Functionsulfurtransferase 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
KOEnzymeEnzyme IDPathwayMap IDSource
K00566mnmA, trmU; tRNA-uridine 2-sulfurtransferaseEC:2.8.1.13
Transfer RNA biogenesisko03016deepkoala

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 Montipora grisea 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 Montipora grisea, 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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