Gene detail

Detailed information of BRAKERKREP00000023037.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:1913697...1917057
NR annotation: GFN28555.1, isoleucine--tRNA ligase [Achromobacter denitrificans]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000023037

ATGCGCGGCGATCTACCTCGCAGAGAGCCCGCATGGATTGCCGCCTGGGAAGAACAACGCATCTACCAAGCCATACGTACCGCCAGTAAAGGCCGCCCTCGCTTCGTGCTGCATGACGGGCCACCCTACGCGAATGGCGATATCCACATTGGCCATGCGGTTAACAAAATCCTGAAGGACATTATTGTCAAAAGCCGCAATATGGCGGGATACGATGCCCATTACGTGCCAGGTTGGGACTGCCACGGCATGCCGATCGAAATCCAGATCGAAAAAAAATACGGCAAGCATTTGCCTGTGGCAGAAGTTCAGTCTAAAGCACGCGCCTATGCATCACAGCAGATCGAGCGGCAGATAAAAGACTTTAAACGGCTCGGCGTGCTGGCCGACTGGGACCGGCCCTACTTGACTATGCATTATGGCAATGAGGCCGATGAGATCCGCGCCTTAGGCCAGATCTTGGAAAAAGGCTATGTGTTTCGTGGCCTGAAGCCTGTTAATTGGTGTTTTGACTGTGCGTCGGCGTTAGCCGAGGCCGAAGTCGAATACGCTGATCGAATCGACCCTGCGGTGGATGTGGCGTTTGCCTTTACCGACCATGCTCGCTTAGCGCAAGCCTTTGGCCTGAAAAAAGTCGACGAGGGCGCTATTGTCATTTGGACAACCACGCCTTGGACCTTGCCCGCAAATCAGGCCCTAAACGTCCATCCCGACATCGACTATGCCTTGGTGCGAGTAAGGCCTACGCCATCCACTGGCCCCCTGTTGCTCGTTGCCCGTGAGCGGGTACCATCCTGTCTGCAACAGTGGCATCTACAAGGCGAAATCATCGCCAGCACCAAAGGCCAAGCGCTGGCAGGACTCACTTTTCAGCATCCTCTGGCTAAGCTTGACGCCGGCTATGCGCGTACAGCGCCCATATACCCAGGCAACTACGTTACCTTAGACACAGGTACTGGCGTCGTGCATTCAGCGCCAGCATATGGGGTAGAGGATTTCATATCGTGCAAAGCGCATGGGCTAGCTGATGCCGACATCATTAACCCCGTACTGGACAATGGTCACTATATTAAGAGCCTGCCCCTGTTTGGCGGGCTCTCTATTTGGGATGCTAACCCCAAAATTGTTGATGCGTTGCAAAGTGCCGGCACGCTTTTGCACATGGAAAAGCATCAGCACAGCTACATGCACTGCTGGCGCCACAAAACACCGGTTATTTACCGAGCCACCAGTCAGTGGTTCGCCGGCATGGACGTTAAGCCCAAGCACGGCGGCCCCAGTCTACGTGAAGCTGCACTCGCCGGTATTGAAGCGACGGCGTTTTATCCCGCCTGGGGCCGCGCGCGCTTGCACGCCATGATCGCCAACCGCCCCGATTGGACCTTATCGAGACAACGGCAATGGGGCGTGCCGATGGCCTTGTTTGTCCATAAAGTGACGGGCGAGTTGCATCCGCGTACGCCAGAACTGCTAGAACAAGTGGCCCAGCGTGTGCAACAAGAGGGCATCGAGGCCTGGCAGCGGCTAGACCCAAGTGAATTGCTGGGTGATGAAGCCgattcatacaaaaaaaacggCGACACACTGGACGTCTGGTTTGATTCTGGCAGCACCCATGCCACCGTGTTAGGTGGCAAAGCGCATGCCTTTGTCGGCTCACACGGCGACGAACTGGCTTGGCCGGCGGATCTTTATCTTGAAGGGTCAGACCAACATCGCGGCTGGTTTCACTCATCACTACTTACTGGCTGCATGCTTTATGGCCAGCCGCCTTATAAAGCTTTGCTCACCCATGGTTTCGTGGTCGACGGCCAAGGCCACAAAATGAGTAAGTCGATCGGCAATATCATTGCGCCGCAAAAAATCGCCGACTCACTGGGTGCAGAAATTTTGCGTCTATGGGTCGCTTCCACCGATTATTCGGGCGAACTGTCGATCTCTGATGAAATCTTAAAGCGAGTGGTTGAAAGTTATCGCCGGATCCGCAATACCCTGCGTTTTTTGTTGGCCAACATAGCTGACTTCGAGGCGACTACCCACGCCGTGCCGTATGACAACTTGCTCGAGATCGACCGTTATGCGCTTTGCTTAACGGAGCAAATGCAGGCCGAGATTTTGGCCAAGTACGAAACTTACGACTTTCATCCGGCCATCGCTCGTCTGCAAACTTTCTGCTCGGAAGACCTGGGGGCGTTTTACCTAGATATTCTTAAAGACCGGCTATACACCACGGCCGCCAACAGTGCGGCGCGCCGCTCGGCGCAGACGGCGCTGCTTGAGATTACGCAGCAGCTGCTCAAACTCATGGCGCCCATTCTCTCCTTTACGGCCGAAGAGGCCTGGCAAGAACTTAGCCGCTCGGCCTTGCGTCTCCAAACGCATACTGCCCGCCCCACCATTTTTACCGAGCTCTACCATCCTGGACCGAACGACGCCGACTCGCACGCTTTAATAACCAAATGGACGCGATTGCGCGCCCTGCGCGGGGAAGTGCTGCGCAAGCTAGAGGAAATTCGCAGCGCGGGTGGCATCGGCGCTTCGCTGCAGGCAGAAGTAGATATACATGCGCCGATGGCAGACCATGAATTGCTTGCCAGCCTGGGCGACGACTTGCGGTTTATGCTTATTGTTTCGCGCGCTACCTTACATACTAGCCCGGGAGAATTACGCATCGAAGTGACGCCTTCCCAGCACAAGAAGTGCGAGCGTTGCTGGCACTGGCGCGCCGACGTGGGACTACAGACTGATCATCCCGAGATTTGCGGCCGTTGTGCCACCAATTTGTTCGGCGCCGGCGAGCTGCGCAACCAGCTTACTAAGCTGTACTTTAATCACCTATTTCAATACGGCGAGCGGCTACAGGTATTGCCAATATTTGACTTAACGCTTATCTACAACCGCGGCGCCGCCTTTAGCTTGCTGGCTTCGCAACCAGGGTGGCAACGATGGTTCTTCATCGCCTTAGGCTTGGGCACTGCGCTACTTATCGTAGGGTTGCTGCGGCGATCATTGAAGCAGCCGCGCTTTTGCTTTGCCCTAGCGCTTATTATGGGCGGGGCGTTAGGCAACGTCCTGGACCGCATGCTCTACGGCCACGTGGTGGactttttactgttttattgGCGCAGCTGGTATTACCCAGCATTCAATTTTGCGGACATAGGAATAACCTGTGGCGCGGTGCTGGCGGTCGTAGACGAAGTGCTGCGCAGCCGCCAGCGTCGCGCCCCTGACTCTTAA

Transcript

BRAKERKRET00000023037

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A9IRC2	Isoleucine--tRNA ligase OS=Bordetella petrii (strain ATCC BAA-461 / DSM 12804 / CCUG 43448) OX=340100 GN=ileS PE=3 SV=1
Q7WKD5	Isoleucine--tRNA ligase OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=ileS PE=3 SV=1
Q7W8Z2	Isoleucine--tRNA ligase OS=Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253) OX=257311 GN=ileS PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002531 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06827 all species →	zf-FPG_IleRS	Zinc finger found in FPG and IleRS	Domain	Interproscan
PF01252 all species →	Peptidase_A8	Signal peptidase (SPase) II	Family	Interproscan
PF08264 all species →	Anticodon_1	Anticodon-binding domain of tRNA ligase	Domain	Interproscan
PF00133 all species →	tRNA-synt_1	tRNA synthetases class I (I, L, M and V)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR033708 all species →	Domain	Isoleucyl tRNA synthetase type 1, anticodon-binding domain	Interproscan
IPR050081 all species →	Family	Isoleucine--tRNA ligase	Interproscan
IPR010663 all species →	Domain	Zinc finger, FPG/IleRS-type	Interproscan
IPR023585 all species →	Family	Isoleucine-tRNA ligase, type 1	Interproscan
IPR001872 all species →	Family	Peptidase A8, signal peptidase II	Interproscan
IPR009080 all species →	Homologous_superfamily	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Interproscan
IPR002301 all species →	Family	Isoleucine-tRNA ligase	Interproscan
IPR013155 all species →	Domain	Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR009008 all species →	Homologous_superfamily	Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain	Interproscan
IPR001412 all species →	Conserved_site	Aminoacyl-tRNA synthetase, class I, conserved site	Interproscan
IPR002300 all species →	Domain	Aminoacyl-tRNA synthetase, class Ia	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR42765 all species →	SOLEUCYL-TRNA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000049 all species →	Molecular Function	tRNA binding	Interproscan
GO:0004822 all species →	Molecular Function	isoleucine-tRNA ligase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006428 all species →	Biological Process	isoleucyl-tRNA aminoacylation	Interproscan
GO:0004190 all species →	Molecular Function	aspartic-type endopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006418 all species →	Biological Process	tRNA aminoacylation for protein translation	Interproscan
GO:0002161 all species →	Molecular Function	aminoacyl-tRNA editing activity	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
K01870	IARS, ileS; isoleucyl-tRNA synthetase	EC:6.1.1.5	Transfer RNA biogenesis	ko03016	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000023037.1 across 29 RNA-seq samples of Hydra viridissima. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

29Samples

7TPM > 0

7Conditions

4.1Max TPM

0.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	0	0.00	0.00
Whole	6	4	2.45	4.13
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	1.45	1.45
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	3.82	3.82
symbioic hydra M9 strain · symbioic hydra rep1	1	1	0.75	0.75
symbioic hydra M9 strain · symbioic hydra rep2	1	0	0.00	0.00
unannotated	1	0	0.00	0.00

Per sample · hover a bar for the full sample record

Show the sample table (29 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	4.13
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	3.98
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	3.56
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	3.00
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.00
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	1.45
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	3.82
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.75
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	0.00
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636	0.00

Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM, StringTie quantification over 29 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Hydra viridissima 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	7	BRAKERKREP00000024957.1	0.990189150404047
Negatively correlated	3	BRAKERKREP00000024112.1	-0.55877800573397

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Hydra viridissima, 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.	ready	open →
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 →