Gene detail

Detailed information of BRAKERIOWP00000005624.1 in Turritopsis rubra

Genomic Location: scaffold270:95486...96887
NR annotation: no NCBI-NR hit recorded
Species Turritopsis rubra · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0019645 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00189 all species →	Ribosomal_S3_C	Ribosomal protein S3, C-terminal domain	Domain	Interproscan
PF00203 all species →	Ribosomal_S19	Ribosomal protein S19	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002222 all species →	Family	Small ribosomal subunit protein uS19	Interproscan
IPR001351 all species →	Domain	Small ribosomal subunit protein uS3, C-terminal	Interproscan
IPR020934 all species →	Conserved_site	Small ribosomal subunit protein uS19, conserved site	Interproscan
IPR023575 all species →	Homologous_superfamily	Small ribosomal subunit protein uS19, superfamily	Interproscan
IPR008991 all species →	Homologous_superfamily	Translation protein SH3-like domain superfamily	Interproscan
IPR018280 all species →	Conserved_site	Small ribosomal subunit protein uS3, conserved site	Interproscan
IPR005704 all species →	Family	Small ribosomal subunit protein uS3, bacterial-type	Interproscan
IPR036419 all species →	Homologous_superfamily	Ribosomal protein S3, C-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11760 all species →	30S/40S RIBOSOMAL PROTEIN S3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0005840 all species →	Cellular Component	ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0022627 all species →	Cellular Component	cytosolic small ribosomal subunit	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 BRAKERIOWP00000005624.1.

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 Turritopsis rubra 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 Turritopsis rubra, 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 →