Detailed information of ANN40816-RA in Montipora grisea

Genomic Location: Scaffold_7863__1_contigs__length_23917:4513...6894
NR annotation: KKS68215.1, Ribonuclease Y [candidate division TM6 bacterium GW2011_GWE2_42_60]
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
A6LSR9Ribonuclease Y OS=Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) OX=290402 GN=rny PE=3 SV=1
Q0SSE8Ribonuclease Y OS=Clostridium perfringens (strain SM101 / Type A) OX=289380 GN=rny PE=3 SV=1
A5N857Ribonuclease Y OS=Clostridium kluyveri (strain ATCC 8527 / DSM 555 / NBRC 12016 / NCIMB 10680 / K1) OX=431943 GN=rny PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0018298 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF12072
all species →
RNase_Y_NRNase Y N-terminal regionCoiled-coilInterproscan
PF01966
all species →
HDHD domainFamilyInterproscan
PF13277
all species →
YmdBYmdB-like proteinDomainInterproscan
PF00013
all species →
KH_1KH domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR022711
all species →
DomainRibonuclease Y, N-terminalInterproscan
IPR006675
all species →
DomainHDIG domainInterproscan
IPR003607
all species →
DomainHD/PDEase domainInterproscan
IPR036612
all species →
Homologous_superfamilyK Homology domain, type 1 superfamilyInterproscan
IPR006674
all species →
DomainHD domainInterproscan
IPR005235
all species →
FamilyMetallophosphoesterase, YmdB-likeInterproscan
IPR004088
all species →
DomainK Homology domain, type 1Interproscan
IPR017705
all species →
FamilyRibonuclease YInterproscan
IPR029052
all species →
Homologous_superfamilyMetallo-dependent phosphatase-likeInterproscan
IPR004087
all species →
DomainK Homology domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR36303
all species →
2',3'-CYCLIC-NUCLEOTIDE 2'-PHOSPHODIESTERASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003723
all species →
Molecular FunctionRNA bindingInterproscan
GO:0004113
all species →
Molecular Function2',3'-cyclic-nucleotide 3'-phosphodiesterase activityInterproscan
GO:0006402
all species →
Biological ProcessmRNA catabolic processInterproscan
GO:0016020
all species →
Cellular ComponentmembraneInterproscan
GO:0003676
all species →
Molecular Functionnucleic acid bindingInterproscan

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 ANN40816-RA.

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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