Gene detail

Detailed information of ENSSJYP00000008387.1 in Catostylus mosaicus

Genomic Location: chr19:5604053...5616486
NR annotation: XP_047122629.1, regulator of nonsense transcripts 2 [Hydra vulgaris]
Species Catostylus mosaicus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSSJYT00000008746

atgaaaccaaaagGCCAACatggaaacaaaaaaacaGACAATACCCATAGATATAGTGCCAGAAGGAACTCTTCAGGCATAAATAAGAACCAGCAAAGcaACGGAAAAGGCAGTTCAAATGATGCAACTAAAGAAGAAgcaaaaactgaaaacaaagaacaacATCCAATAGAAGAGGTTGCAACTACCCCAGAAGCAGAGGAAAAGAGTGAAGATGCTTCATTAGTCAATGAAGATGCTGAGGTGCTATTAGAGATTGAGAAGaaccaagcacttgaAGCTCAAGAGAGTGCCAAAGAACGAATCAACGCAAGAAATGCTATCAGAGAGAAAAATCTTGCTGCCCTTGatCATTGCCCTGAAGATACATTTTTTAAGAAGTTAGATTCGTCCATGAGAAAGAATACAGCATTTGTTAAGAAACTGAAAAATGTCACAGAGCAGCAAAGAGAATCCTTAGGGCAAGAATTCAATGGTTTGAATTTGACAAAGTTTATCCAAGAAGCTGTAAATTCAATTGTTGAAGCAAAGATCAAGGTTGCCGATGTTGGTTGCGTGGCTCATTTATGCAGCCTATTCCATCAAAGATATGCAGAATTCACGCCactgttgaaaaatttgatagagaaatcatttgaaaacataAATTGCAAGGATGATGATAAGGTTGCAAATGTTCCAAGACTGCGTTCGTCTTTACGACTTATCACCGAGCTTATCCTTAATGGTGTGTTTACAAATGTTGATGAGAGTGTAAAACTGCTGCATAGTATTATTCTGTCAATTGTCAACTCTGATACGACGTCTCACGTGTATGCTCCGGTTATACTGACATTTGTAAGACACTGCGGAGGCGATGTCATCGGAATAATGCCAAGAAAACAAAGgaTATGGAAGGAGAAGTTCAACATGGAATTTATGCAGTGCAATGTAATACCACAAAATTTCAAGACAACGTTCAGAGatctttttaaagaatatttcgATTCGATGGCAAAACATCTAGTCAGAGATCATAAATCATTACAAAACAGAGAAAGACAAAATCGACAAACAATAGGGTTAAAAGGTGAACTATCTTCAGAGCGCAAAGAAGCATGTGAAAAAGCGCAGAAGTCATATGAGAAACTGCTGGCAAACACAACCTCTTTAGCGGAATGGCTCGATGAAGAAATCCCAGATCTACCTGAAGATCAGTTCGAAGAGAAAGATGAACCTGGAACTATCAACATATTCACTCCAGTCAGAGGAACCGAATATGACACTGAAAATGGATTATGGGAAGATGAAGATACGAGAACATTTTACGAGAATTTGAAAGATCTCAAAGCATTTGTACCTCAGattttattcaaagagaaAGAGACAAAGCCGTCgaaagataataaaaaagatcaaaaaaaGAAACGGAAATTAAGAAACGATCTTAATCTTAATGATGATTTCATGGACGATTTCAGTGACGATGATTTGGGTGATAATtacgaaaaagaaattttaggcGATGAAACTGAGGATAACGATGCATCTGGTAACAATTCATCTGGGACAAATATGGCCCAAATAGTGGAACAATATCTACAAAACCTTGTAAATTGTGTAAATAGAGACTTCATAGATCAGGCCGCAGAGACGtttatcatgaaaatgaatcgaaaagataacagaaagaaattaatcaaatcGTTGTTTTCTGTAAGTCGAACAAGGCTGGATCTACTTCCATTTTATGGTCGTTTGGTTGCCACATTAGCCCCATGCTTGCCAGATATTGCCCAAGATTtgattttcttgcttaaaGGAGATTTCAGATTTCACttcAGAAAGAAGCATCAGATTAATCTGGAATCAAAAGTCAAAACAGTTCGCTTTATTGGAGAACTGACcaaatttaaagtttgtcCAAAAGCCGAAGCTCTCCATTGCTTAAAGATGCTTCTTGAAGACTTCACGCATCATAATATTGAGATGGCTTGTCATTTGCTGGAAACATGTGGAAGATTTTTATACCGATCACCAGAATCGCATCCTAGAATGATTAAGCTGCTGGAACAAATGATGCGCAAGAAAGCAGTTCAGACTATGGATTCAAGATTATCAACAATGATCGAGAATGCTTATTATTATTGCAACCCACCTGAGAGACAAAAAGTACAAGTGAAAGAAAGGCCACCAATGCATGAGTATATACGAAAACTACTTTACAAAGACTTGTCTAAAAcaacaacagaaaaagtgcTGAGACAAATGCGCAAACTGCCATGGCAAGAACCAGGGATCAAAGAGTATGCTGTGAAATGTTTGACACGTGTCTGGAACATCAAGTACAGTAACATCCATTGTGCTGCAAACATGCTCTCTGGTTTGTGTGAATACCATGATGATCTTGGTGTTTTCGTTGTTGATGAAGTTATTGAGCATATAAGGCTAGGAATGGAGatcAACATTCATAAATTCAATCAGCAGCGAGTTAGCATGATAAAATACCTTGGGGAATTGTTTAATTACCAACTAGTCGAGACAGAAGTCATTTTCACCACTTTGTATTCATTGATCACCTTTGGAAACAGCGGAGAT

Transcript

ENSSJYT00000008746

ataaGATCAAATTGGTGGcaaaatgaaaccaaaagGCCAACatggaaacaaaaaaacaGACAATACCCATAGATATAGTGCCAGAAGGAACTCTTCAGGCATAAATAAGAACCAGCAAAGcaACGGAAAAGGCAGTTCAAATGATGCAACTAAAGAAGAAgcaaaaactgaaaacaaagaacaacATCCAATAGAAGAGGTTGCAACTACCCCAGAAGCAGAGGAAAAGAGTGAAGATGCTTCATTAGTCAATGAAGATGCTGAGGTGCTATTAGAGATTGAGAAGaaccaagcacttgaAGCTCAAGAGAGTGCCAAAGAACGAATCAACGCAAGAAATGCTATCAGAGAGAAAAATCTTGCTGCCCTTGatCATTGCCCTGAAGATACATTTTTTAAGAAGTTAGATTCGTCCATGAGAAAGAATACAGCATTTGTTAAGAAACTGAAAAATGTCACAGAGCAGCAAAGAGAATCCTTAGGGCAAGAATTCAATGGTTTGAATTTGACAAAGTTTATCCAAGAAGCTGTAAATTCAATTGTTGAAGCAAAGATCAAGGTTGCCGATGTTGGTTGCGTGGCTCATTTATGCAGCCTATTCCATCAAAGATATGCAGAATTCACGCCactgttgaaaaatttgatagagaaatcatttgaaaacataAATTGCAAGGATGATGATAAGGTTGCAAATGTTCCAAGACTGCGTTCGTCTTTACGACTTATCACCGAGCTTATCCTTAATGGTGTGTTTACAAATGTTGATGAGAGTGTAAAACTGCTGCATAGTATTATTCTGTCAATTGTCAACTCTGATACGACGTCTCACGTGTATGCTCCGGTTATACTGACATTTGTAAGACACTGCGGAGGCGATGTCATCGGAATAATGCCAAGAAAACAAAGgaTATGGAAGGAGAAGTTCAACATGGAATTTATGCAGTGCAATGTAATACCACAAAATTTCAAGACAACGTTCAGAGatctttttaaagaatatttcgATTCGATGGCAAAACATCTAGTCAGAGATCATAAATCATTACAAAACAGAGAAAGACAAAATCGACAAACAATAGGGTTAAAAGGTGAACTATCTTCAGAGCGCAAAGAAGCATGTGAAAAAGCGCAGAAGTCATATGAGAAACTGCTGGCAAACACAACCTCTTTAGCGGAATGGCTCGATGAAGAAATCCCAGATCTACCTGAAGATCAGTTCGAAGAGAAAGATGAACCTGGAACTATCAACATATTCACTCCAGTCAGAGGAACCGAATATGACACTGAAAATGGATTATGGGAAGATGAAGATACGAGAACATTTTACGAGAATTTGAAAGATCTCAAAGCATTTGTACCTCAGattttattcaaagagaaAGAGACAAAGCCGTCgaaagataataaaaaagatcaaaaaaaGAAACGGAAATTAAGAAACGATCTTAATCTTAATGATGATTTCATGGACGATTTCAGTGACGATGATTTGGGTGATAATtacgaaaaagaaattttaggcGATGAAACTGAGGATAACGATGCATCTGGTAACAATTCATCTGGGACAAATATGGCCCAAATAGTGGAACAATATCTACAAAACCTTGTAAATTGTGTAAATAGAGACTTCATAGATCAGGCCGCAGAGACGtttatcatgaaaatgaatcgaaaagataacagaaagaaattaatcaaatcGTTGTTTTCTGTAAGTCGAACAAGGCTGGATCTACTTCCATTTTATGGTCGTTTGGTTGCCACATTAGCCCCATGCTTGCCAGATATTGCCCAAGATTtgattttcttgcttaaaGGAGATTTCAGATTTCACttcAGAAAGAAGCATCAGATTAATCTGGAATCAAAAGTCAAAACAGTTCGCTTTATTGGAGAACTGACcaaatttaaagtttgtcCAAAAGCCGAAGCTCTCCATTGCTTAAAGATGCTTCTTGAAGACTTCACGCATCATAATATTGAGATGGCTTGTCATTTGCTGGAAACATGTGGAAGATTTTTATACCGATCACCAGAATCGCATCCTAGAATGATTAAGCTGCTGGAACAAATGATGCGCAAGAAAGCAGTTCAGACTATGGATTCAAGATTATCAACAATGATCGAGAATGCTTATTATTATTGCAACCCACCTGAGAGACAAAAAGTACAAGTGAAAGAAAGGCCACCAATGCATGAGTATATACGAAAACTACTTTACAAAGACTTGTCTAAAAcaacaacagaaaaagtgcTGAGACAAATGCGCAAACTGCCATGGCAAGAACCAGGGATCAAAGAGTATGCTGTGAAATGTTTGACACGTGTCTGGAACATCAAGTACAGTAACATCCATTGTGCTGCAAACATGCTCTCTGGTTTGTGTGAATACCATGATGATCTTGGTGTTTTCGTTGTTGATGAAGTTATTGAGCATATAAGGCTAGGAATGGAGatcAACATTCATAAATTCAATCAGCAGCGAGTTAGCATGATAAAATACCTTGGGGAATTGTTTAATTACCAACTAGTCGAGACAGAAGTCATTTTCACCACTTTGTATTCATTGATCACCTTTGGAAACAGCGGAGATGG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A2AT37	Regulator of nonsense transcripts 2 OS=Mus musculus OX=10090 GN=Upf2 PE=1 SV=1
Q9HAU5	Regulator of nonsense transcripts 2 OS=Homo sapiens OX=9606 GN=UPF2 PE=1 SV=1
F4IUX6	Regulator of nonsense transcripts UPF2 OS=Arabidopsis thaliana OX=3702 GN=UPF2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003459 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02854 all species →	MIF4G	MIF4G domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR003890 all species →	Domain	MIF4G-like, type 3	Interproscan
IPR039762 all species →	Family	Nonsense-mediated mRNA decay protein Nmd2/UPF2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12839 all species →	NONSENSE-MEDIATED MRNA DECAY PROTEIN 2 UP-FRAMESHIFT SUPPRESSOR 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005844 all species →	Cellular Component	obsolete polysome	Interproscan
GO:0035145 all species →	Cellular Component	exon-exon junction complex	Interproscan

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 ENSSJYP00000008387.1.

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 Catostylus mosaicus 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 Catostylus mosaicus, 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.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search 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 found	open →
Expression heatmap	Draw 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 / orthogroup	Look 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 analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →