Detailed information of ENSVBPP00000026428.1 in Meandrina meandrites

Genomic Location: chr2:26563872...26578417
NR annotation: XP_027050397.1, tRNA:m(4)X modification enzyme TRM13 homolog isoform X1 [Pocillopora damicornis]
Species Meandrina meandrites · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q8BYH3tRNA:m(4)X modification enzyme TRM13 homolog OS=Mus musculus OX=10090 GN=Trmt13 PE=2 SV=1
Q9NUP7tRNA:m(4)X modification enzyme TRM13 homolog OS=Homo sapiens OX=9606 GN=TRMT13 PE=1 SV=2
Q6C4F8tRNA:m(4)X modification enzyme TRM13 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) OX=284591 GN=TRM13 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004276 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF05206
all species →
TRM13Methyltransferase TRM13FamilyInterproscan
PF11722
all species →
zf-TRM13_CCCHCCCH zinc finger in TRM13 proteinDomainInterproscan
PF05253
all species →
zf-U11-48KU11-48K-like CHHC zinc fingerDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR022776
all species →
DomainTRM13/UPF0224 family, U11-48K-like CHHC zinc finger domainInterproscan
IPR007871
all species →
DomainMethyltransferase TRM13Interproscan
IPR021721
all species →
DomainZinc finger, CCCH-type, TRM13Interproscan
IPR039044
all species →
FamilytRNA:m(4)X modification enzyme Trm13Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12998
all species →
UNCHARACTERIZEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0008033
all species →
Biological ProcesstRNA processingInterproscan
GO:0008168
all species →
Molecular Functionmethyltransferase activityInterproscan
GO:0008175
all species →
Molecular FunctiontRNA methyltransferase activityInterproscan
GO:0030488
all species →
Biological ProcesstRNA methylationInterproscan
GO:0106050
all species →
Molecular FunctiontRNA 2'-O-methyltransferase 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
K15446TRM13, CCDC76; tRNA:m4X modification enzymeEC:2.1.1.225
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 Meandrina meandrites 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 Meandrina meandrites, 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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