Gene detail

Detailed information of ENSCIQP00000006473.1 in Millepora alcicornis

Genomic Location: chr13:104884608...104930665
NR annotation: XP_012564686.2, threonine--tRNA ligase 1, cytoplasmic isoform X2 [Hydra vulgaris]
Species Millepora alcicornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSCIQT00000007633

atgaatattaacGAGAAACCAGCCCAGAAACAGCAAGGAAGCtccaaaaaggagaaaaagaagaaagagaaaaacaaagaTGATGGTGGAACATCAGGTTTTCCGGTGGAGCTCAATCCACCACCAGCATATTTACAAGAACGTATCAAATTTTTTGACCAACTGAAATTAGAGTATGATGCTGAAGTTGAAgCCAAACCAAAACCACCAATAAAAGTTTTACTGCCAGATGGTAAAGAAGTAGAAGGAGTAGCATGGAAAACAACACCATATGAAATTGCTCAAGGAATCAGCCAAGGTCTTGCAGATAATGCTGTTATTGCCAAGgTCAATGGTGTCTTATGGGATTTGGATAGGGCTTTAGAAGAAGACAGCAAAGTTGAAATCTTGAAGTTTGATAATACTGAAGgTCAGCAAGTGTTTTGGCATTCAAGTGCTCATATACTTGGCGAAGCCATGGAAAGGCATTATGGAGGATGTTTATGTTATGGTCCACCAATAGAAGAAGGATTCTACTATGACATGGCTCTCGAAGGACGCCAAGTGTCAAGTAACGATTTCGGTAAATtagaaactatattaaaaaaagcaataaaagaaaagCAGCCATTTAtcagattagaaatgaaaaaggaagatttactaaaaatgtttgctTATAATCCATACAAAGTCCGAATATTGAATGAAAAAGTCACCAGTCCAACTACTACTGTGTACAGGTGTGGACCACTAATAGATTTATGCAGAGGACCTCATGTAAGACACACTGGTAAAGTAAAGGCAATGAGCATCACAAAGAATTCTGCCACGTATTGGGAAGGAAATGCTGATGCTGAATCTCTGCAAAGGATATATGGAATATCATTCCCAAACGATAAAATGTTAAAAGAGTGGAAACATTTCCAAGAGGAGGCAGCAAAGAGAGATCACAGGAAGCTTGGAAGAGAGCAAGAGTTATTTTTCTTCCATGAACTGAGTCCAGGATCATGTTTCTTCTTACCAAATGGTGCACATATCTTTAATACGTTGGTAAAATTTATTAGGTCAGAATATCAAAAACGAGGATTCCAAGAAGTTGTGACTCCAAATATATATAGCACAAAACTTTGGGAGACTTCTGGGCATTGGCAACATTATTCGacaaatatgttttcttttgaagTGGAAAAAGAAAGATATGCATTAAAACCAATGAATTGCCCAGGTCACTGTGTAATGTTCGACCACCGTCCTCGTTCTTGGCGTGAACTGCCGCTACGAATGGCGGATTTTGGAGTACTACATCGTAACGAATTGTCAGGCACACTAACTGGTTTGACTCGTGTGCGGCGTTTCCAACAAGACGATGCACATATCTTTTGTACTATGGACCAGGTGGAATCGGAAATCGAAGGTTGTCTAGACTTTCTCCGCCATGTTTACTCAATCTTTGGTTTCACCTTCAAGTTATACTTATCCACCCGTCCGgataaatatttaggagaaatcgAGAAATGGAATCGTGCTGAAAAGCAATTAGAAAATTCTTTGAACTCATTTGGTGAACCATGGGAACTGAATCCAGGAGATGGGGCATTCTACGGACCCAAGATTGACATCCAAATTCGTGATGCATTAAGGCGTTACCATCAATGTGCTACAATTCAACTTGACTTTCAATTACCAGAGAGATTTAATTTACATTACGTCAGTGGTGAAGGGGATGAGAAGAAACGACCTGTTATCATTCACAGGGCAGTTCTTGGTTCTGTTGAAAGAATGATGGCGATTCTAACCGAGAACTTTGGTGGAAAGTGGCCGTTTTGGCTATCTCCACGTCAAGCAATCGTCATACCCGTTAGCCCAAAATTTGATGACTACGCAAAGAAGGTGCACAGCAAGATCCATGCACAGTGCTACAAAATTGATATGAATTTGGATACAGGTGAAACTCTGAACAAGAAAATTCGAAATGCTCAGTTAGCTCAGTACAACTTCATTTTAGtTGTTGGAGACAAGGaaatgacatcatcaactgtgaATGTTCGAACTCGGGATAATAAAGTTCATGGGGAAAAATCACTCGACGCTCTACTCGCTCGATTTGAGAAACTTCAAGAGACGAAAGAAGATCATAGTGAAGATGATTTCTag

Transcript

ENSCIQT00000007633

tatgaatattaacGAGAAACCAGCCCAGAAACAGCAAGGAAGCtccaaaaaggagaaaaagaagaaagagaaaaacaaagaTGATGGTGGAACATCAGGTTTTCCGGTGGAGCTCAATCCACCACCAGCATATTTACAAGAACGTATCAAATTTTTTGACCAACTGAAATTAGAGTATGATGCTGAAGTTGAAgCCAAACCAAAACCACCAATAAAAGTTTTACTGCCAGATGGTAAAGAAGTAGAAGGAGTAGCATGGAAAACAACACCATATGAAATTGCTCAAGGAATCAGCCAAGGTCTTGCAGATAATGCTGTTATTGCCAAGgTCAATGGTGTCTTATGGGATTTGGATAGGGCTTTAGAAGAAGACAGCAAAGTTGAAATCTTGAAGTTTGATAATACTGAAGgTCAGCAAGTGTTTTGGCATTCAAGTGCTCATATACTTGGCGAAGCCATGGAAAGGCATTATGGAGGATGTTTATGTTATGGTCCACCAATAGAAGAAGGATTCTACTATGACATGGCTCTCGAAGGACGCCAAGTGTCAAGTAACGATTTCGGTAAATtagaaactatattaaaaaaagcaataaaagaaaagCAGCCATTTAtcagattagaaatgaaaaaggaagatttactaaaaatgtttgctTATAATCCATACAAAGTCCGAATATTGAATGAAAAAGTCACCAGTCCAACTACTACTGTGTACAGGTGTGGACCACTAATAGATTTATGCAGAGGACCTCATGTAAGACACACTGGTAAAGTAAAGGCAATGAGCATCACAAAGAATTCTGCCACGTATTGGGAAGGAAATGCTGATGCTGAATCTCTGCAAAGGATATATGGAATATCATTCCCAAACGATAAAATGTTAAAAGAGTGGAAACATTTCCAAGAGGAGGCAGCAAAGAGAGATCACAGGAAGCTTGGAAGAGAGCAAGAGTTATTTTTCTTCCATGAACTGAGTCCAGGATCATGTTTCTTCTTACCAAATGGTGCACATATCTTTAATACGTTGGTAAAATTTATTAGGTCAGAATATCAAAAACGAGGATTCCAAGAAGTTGTGACTCCAAATATATATAGCACAAAACTTTGGGAGACTTCTGGGCATTGGCAACATTATTCGacaaatatgttttcttttgaagTGGAAAAAGAAAGATATGCATTAAAACCAATGAATTGCCCAGGTCACTGTGTAATGTTCGACCACCGTCCTCGTTCTTGGCGTGAACTGCCGCTACGAATGGCGGATTTTGGAGTACTACATCGTAACGAATTGTCAGGCACACTAACTGGTTTGACTCGTGTGCGGCGTTTCCAACAAGACGATGCACATATCTTTTGTACTATGGACCAGGTGGAATCGGAAATCGAAGGTTGTCTAGACTTTCTCCGCCATGTTTACTCAATCTTTGGTTTCACCTTCAAGTTATACTTATCCACCCGTCCGgataaatatttaggagaaatcgAGAAATGGAATCGTGCTGAAAAGCAATTAGAAAATTCTTTGAACTCATTTGGTGAACCATGGGAACTGAATCCAGGAGATGGGGCATTCTACGGACCCAAGATTGACATCCAAATTCGTGATGCATTAAGGCGTTACCATCAATGTGCTACAATTCAACTTGACTTTCAATTACCAGAGAGATTTAATTTACATTACGTCAGTGGTGAAGGGGATGAGAAGAAACGACCTGTTATCATTCACAGGGCAGTTCTTGGTTCTGTTGAAAGAATGATGGCGATTCTAACCGAGAACTTTGGTGGAAAGTGGCCGTTTTGGCTATCTCCACGTCAAGCAATCGTCATACCCGTTAGCCCAAAATTTGATGACTACGCAAAGAAGGTGCACAGCAAGATCCATGCACAGTGCTACAAAATTGATATGAATTTGGATACAGGTGAAACTCTGAACAAGAAAATTCGAAATGCTCAGTTAGCTCAGTACAACTTCATTTTAGtTGTTGGAGACAAGGaaatgacatcatcaactgtgaATGTTCGAACTCGGGATAATAAAGTTCATGGGGAAAAATCACTCGACGCTCTACTCGCTCGATTTGAGAAACTTCAAGAGACGAAAGAAGATCATAGTGAAGATGATTTCTagatttttagcaaattatttaatttagtaattattaccatttatttaatataataaaattattagaagtgttttagaagcatatcataaacAAGAAGCTTTGTTATGTTGCTACCTTTAAAGTCGGAAGTTTTTGGCCAGTATAATATAAAGTCAcgacatatttgaaaaaaaaaactgcaatTTGGAGGGGATTCTCGACGGATCAAATATacctataaaaaagttttgatttgtttttattagatttaggCGTGGCTTTTATTGTTCTAAGTCAATGTTTCTTTCCGAAGCTCAAACTTCACGTTTTAAAAAAATCGTGAAATGATTTTTGCTGCATTGTGTTTCTATTCACTTCAGCTCAAAAAAGTGtggttcatatttttaaaattgtttcaaactgg

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3ZBV8	Threonine--tRNA ligase 1, cytoplasmic OS=Bos taurus OX=9913 GN=TARS1 PE=2 SV=1
Q9D0R2	Threonine--tRNA ligase 1, cytoplasmic OS=Mus musculus OX=10090 GN=Tars1 PE=1 SV=2
Q5XHY5	Threonine--tRNA ligase 1, cytoplasmic OS=Rattus norvegicus OX=10116 GN=Tars1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002436 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07973 all species →	tRNA_SAD	Threonyl and Alanyl tRNA synthetase second additional domain	Domain	Interproscan
PF02824 all species →	TGS	TGS domain	Domain	Interproscan
PF03129 all species →	HGTP_anticodon	Anticodon binding domain	Domain	Interproscan
PF00587 all species →	tRNA-synt_2b	tRNA synthetase class II core domain (G, H, P, S and T)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012947 all species →	Domain	Threonyl/alanyl tRNA synthetase, SAD	Interproscan
IPR036621 all species →	Homologous_superfamily	Anticodon-binding domain superfamily	Interproscan
IPR012676 all species →	Homologous_superfamily	TGS-like	Interproscan
IPR004095 all species →	Domain	TGS	Interproscan
IPR002320 all species →	Family	Threonine-tRNA ligase, class IIa	Interproscan
IPR018163 all species →	Homologous_superfamily	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily	Interproscan
IPR006195 all species →	Domain	Aminoacyl-tRNA synthetase, class II	Interproscan
IPR004154 all species →	Domain	Anticodon-binding	Interproscan
IPR045864 all species →	Homologous_superfamily	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Interproscan
IPR047246 all species →	Domain	Threonine-tRNA ligase, class IIa, anticodon-binding domain	Interproscan
IPR002314 all species →	Domain	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Interproscan
IPR012675 all species →	Homologous_superfamily	Beta-grasp domain superfamily	Interproscan
IPR033728 all species →	Domain	Threonine-tRNA ligase catalytic core domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11451 all species →	THREONINE-TRNA LIGASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
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:0004829 all species →	Molecular Function	threonine-tRNA ligase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006435 all species →	Biological Process	threonyl-tRNA aminoacylation	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0006418 all species →	Biological Process	tRNA aminoacylation for protein translation	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
K01868	TARS, thrS; threonyl-tRNA synthetase	EC:6.1.1.3	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 Millepora alcicornis 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 Millepora alcicornis, 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 →