Detailed information of ANN24601-RA in Montipora grisea

Genomic Location: Scaffold_66__1_contigs__length_383707:172082...173758
NR annotation: WP_200605931.1, ribonuclease J [Thermohalobaculum xanthum]
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
M4MR97Ribonuclease J OS=Sinorhizobium meliloti (strain Sm2011 / Rm2011 / 2011) OX=1286640 GN=rnj PE=3 SV=1
P54122Ribonuclease J OS=Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534) OX=196627 GN=rnj PE=3 SV=2
Q49WL3Ribonuclease J 1 OS=Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229 / NCIMB 8711 / NCTC 7292 / S-41) OX=342451 GN=rnj1 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0018307 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00753
all species →
Lactamase_BMetallo-beta-lactamase superfamilyDomainInterproscan
PF17770
all species →
RNase_J_CRibonuclease J C-terminal domainDomainInterproscan
PF07521
all species →
RMMBLZn-dependent metallo-hydrolase RNA specificity domainMotifInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR042173
all species →
Homologous_superfamilyRibonuclease J, domain 2Interproscan
IPR001279
all species →
DomainMetallo-beta-lactamaseInterproscan
IPR036866
all species →
Homologous_superfamilyRibonuclease Z/Hydroxyacylglutathione hydrolase-likeInterproscan
IPR041636
all species →
DomainRibonuclease J, C-terminalInterproscan
IPR011108
all species →
DomainZn-dependent metallo-hydrolase, RNA specificity domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR43694
all species →
RIBONUCLEASE JInterproscan

 Gene Ontology
No Gene Ontology signature was recorded for ANN24601-RA in Montipora grisea.
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
K12574rnj; ribonuclease JEC:3.1.-.-
Messenger RNA biogenesisko03019deepkoala

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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