Gene detail

Detailed information of BRAKERIOWP00000003893.1 in Turritopsis rubra

Genomic Location: scaffold160:138375...147253
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

BRAKERIOWT00000003893

ATGCCAGATTATCGTTGTACCAAAGAAATTCGTCAAGGATTTATTGATTTCTTCGTCAACAAGTACCGGCACACATTTGTTCCATCTTCATCAACTATTCCACATGAAGATCCTACTCTACTTTTCGCTAATGCAGGAATGAATCAGttCAAATCATGTTTCTTGGGTACTGTCGATCCAAATAGTGACCTAGCAAAGATAACCCGTGTGGTCAATTCCCAAAAATGCATCCGTGCTGGCGGAAAGCATAATGATTTAGATGATGTCGGCAAAGATGTTTACCATCACACTTTCTTTGAAATGCTTGGTAATTGGTCATTTGGGGATTTTTTCAAGAAAGAAATCATTGCATGGTCGTGGGAGTTACTTACAGAAGTGTGGGGATTGGATAAAGATAGGTTTTATGCTACTTATTTCGGTGGCACGGACAGTGTACCAGCTGATGAAGAAGCCAGACAATTTTGGATTGATACAGGtatTCCAACAAATCGTGTTCTTCCTTTTGGAATGAAAgataacttttgggagatgGGAGATACTGGCCCTTGTGGTCCTTGCTCCGAATTGCATTATGATCGTATAGGTGGGAGAGATGCTTCACATCTTGTCAATATGGATGTCCCTGAAGTTTTAGAAGTTTGGAACCTTGTTTTTATACAGTTTAACAGAGAAAGTGATGGTACTCTGGTACCATTGCCCAGCAAACATGTTGATACTGGAATGGGATTAGAAAGGATTGTTTCTGTTATTCAATCCAAAATGTCTAACTATGACACAGACATATTTACCCCATTTTTTGAAACCATTCATAAGGGTACTGGAACTAGGCCGTACAGTGGTTTAATTGGTGCAGAAGACAAGGACGGGATTGATATGGCATACAGGGTAGTTGCTGATCATATTCGTACATTGACCATTGCCTTGTCTGATGGTGGAAGACCAGATAACATGGGGAGaggATATGTATTACGACGTATTTTAAGAAGAGGTATTCGATATGGCAGTGAAAAATTAAACTGTCAACCTGGTTTTCTTGCTTCACTGGTTGATGTAGTTTGTGAAACCCTCGGTGAACCATTTCCAGGCTTATTGAAAGATCCACAGAcgATAAAAGATATTATCAACGAAGAGGAAACTCAATTTCTGAAAACTTTAAATCGTGGACGAAGACTTTTCAACAGAGCTGCTGATAAAGCTACCAATGGTAAAATTGAAGGTGAAATTGCTTGGCGATTATACGATACTTACGGATTTCCTGTTGATTTGACTGTGCTAATGGCTGAAGAGAGAAATCTTATTGTTGATATGCAAGCGTATGAAgaatcaaaattaaaagcacAAGAAATGGCTCGTGCAAAGGGTAGTGGCACCGAAGATTTGTGCACTTTGGATGTGTATGCACTGGATGAGTTGAAATCGAAAGGGTTCGCCCAAACTGATGAATTACCCAAATACAATTacgataatgataatgatggaATTTATACATTCCACCCAACTTATGCGACAGTGAAGGCGTTGCGAATAAATAAGCAGTTTGCTGATCGAGTGACCAGTGGTAACCGGTGTGGTATTGTGTTAGATAAGACATGTTTTTACGCTGAACAAGGAGGCCAGTTGTATGATACCGgatatgtaaacaaagacGGCGACGAGGATGTGGAGTTCGTTGTTGAAGATGTGCAGGTTCATGGTGGCTATGTGATACATATTGGCCAGTTGGAAGGTGTGCTTCAAGTAGGCGATAAAGTGAAGTGTACTATAGATGAAGAACGAAGAAGAACTTTGATGAACAACCATACTGGTACACATCTGTTAAATTTTGCTTTAAGACAAGTGTTGGGTGAGGCCGACCAACGAGGTTCACTCGTGGCGCCTGATAAACTAAGATTCGATTTTACTGCGAAGagagcAATGACAACAGAACAAGTGAAAGAAGCAGAAAGTATTACTCGGAATCTTGTTAATAATAAGCAACCTGTGCATGCAACAGTGAGTTCTTTGGCTGTTGCTAAAGATATAAAAGGATTAAGAGCTATCTTCGATGAGGTGTATCCCGACCCTGTTCGTGTTATATCAATTCATCACACGTTAGAAGATTTGGTGAACGATCCACAAGCTGGTTTTAAAACATCAATCGAGTTCTGTGGTGGAACGCATTTGAAGAATACTGGCGACATGACGGAGTTTGCAATCGTTTCTGAGGAAGCCATTTCTAAAGGAATTCGAAGAATTGTAGCGGTTACTGGTAATGATGCTTTGAAGGCACATAAGAAAGCTAGCCAGCTTGAAGAAGATTTgcagaaatttgaaaaagaaactgaaCAGCAGAAAAATATATGTACATTGAATTATAAACAGCTGACTCAGCAGATTGCTCGAATGAACGATGAGATATCTGAATCGACAATACCTGCTTggaaaaaagataatatacgtaataacttgaaaaatattaaaaaatcgTTAGATGATGCAGAGCGTGCTTATAAAGCTGGGAAAATGCAGAGGgTGGTTGAAAAAGCTGGCGAAATCTCCAAAGCGGCTCAAGATAAATCATTTATTGTCGAACGTGTCGAGGACAGTTGCCATGCAaagGCTCTAGATGCTGCCTTGAAGCAAGTGAAAAACAACGGACCGCATTTAGCTGCTATGTTATTCTCCCTTGATAAGGAAACAAACAAAGTGTTGTACCTTTGTCAAGTTCCCAAGGGTGTTGTTGACGAAAAAGGATTGAAAGCCGATGAATGGGTGAAAAAAGTCGCGACCGTGATTGGTGGAAAGGGCGGAGGCAAACCAATCAGTGCTCAAGGTTCAGGTGATAACCTTGAGGGCATAGACAAAGCTATAGAAATTGCAACAGAGTTTGCTCacttaaaactttcttaa

Transcript

BRAKERIOWT00000003893

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002674 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02272 all species →	DHHA1	DHHA1 domain	Family	Interproscan
PF01411 all species →	tRNA-synt_2c	tRNA synthetases class II (A)	Family	Interproscan
PF07973 all species →	tRNA_SAD	Threonyl and Alanyl tRNA synthetase second additional domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045864 all species →	Homologous_superfamily	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Interproscan
IPR050058 all species →	Family	Alanine--tRNA ligase	Interproscan
IPR012947 all species →	Domain	Threonyl/alanyl tRNA synthetase, SAD	Interproscan
IPR023033 all species →	Family	Alanine-tRNA ligase, eukaryota/bacteria	Interproscan
IPR002318 all species →	Family	Alanine-tRNA ligase, class IIc	Interproscan
IPR018165 all species →	Domain	Alanyl-tRNA synthetase, class IIc, core domain	Interproscan
IPR003156 all species →	Domain	DHHA1 domain	Interproscan
IPR018162 all species →	Homologous_superfamily	Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily	Interproscan
IPR018164 all species →	Domain	Alanyl-tRNA synthetase, class IIc, N-terminal	Interproscan
IPR009000 all species →	Homologous_superfamily	Translation protein, beta-barrel domain superfamily	Interproscan
IPR018163 all species →	Homologous_superfamily	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11777 all species →	ALANYL-TRNA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0002161 all species →	Molecular Function	aminoacyl-tRNA editing activity	Interproscan
GO:0004813 all species →	Molecular Function	alanine-tRNA ligase activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006419 all species →	Biological Process	alanyl-tRNA aminoacylation	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0043039 all species →	Biological Process	tRNA aminoacylation	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K01872	AARS, alaS; alanyl-tRNA synthetase	EC:6.1.1.7	Transfer RNA biogenesis	ko03016	deepkoala

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 →