Gene detail

Detailed information of BRAKERKREP00000001227.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047126079.1, leucine--tRNA ligase, cytoplasmic-like [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000001227

ATGAATGGTAAACTTCACCTGGGTCACACCTTCACTATTTCTAAGGCAgagtttGCAGTGGGATTCCAAAGACTGAAAGGCAAAAGATGTTTATTCCCATTTGGTTTTCATTGCACAGGAATGCCTAttaagGCATGTGCTGATAAGTTGAAGAGAGAAATAGAGGATTATGGCTGTCCGCCTGTTTTTCCAAGTGAAGCAGAGAAAAAAGACATAAGcaattTGAAAAGTAAAGTTGCAGCTAAGACCGGTGGGTTAACATATCAATGGCAGATCATGCAAGCACTTGATATACCTGATgacttaattaaaaatttttctgaaCCTGATTTCTGGTTGGAATATTTTCCACCTCTAGCCATTAAAGACTTAAAATCTATGGGgttaaaagtGGATTGGAGGAGATCATTTATTACAACTGATGCCAACCCCTATTACGATTCATTTGCTAAATggcattttaacaaacttaaaagtttaggaaaaatcaaatttggaaaaagGTATACAATCTATTCAACTCTTGACAACCAACCTTGCATGGATCATGATCGTTTATCAGGAgaagGTGTAGCACCTCAAGAGTACACTTTGATTAAAATGCAAGTTGTTGAGCCACTCCCACAAAGTTTGAGTACTTTAGAGGGCAAGAAAGTTTTCCTAGTTGCTGCTACACTGAGACCTGAAACGATGTATGGGCAAACAAACTGCTGGATTCATCCAGAAATAgaaTATATTGCATTTGCATCATCAACTGAAAATGAGGTTTATATAAGCACAGAGAGAGCTGCAAAAAATATGGCTTACCAAGGCTTAACTCAAAAAGATAACCATGTAGATATTCTATTACAGTTATTAGGGATGGATATAATGGGAATAGCATTAAATGCACCATTAACATCAAATAAGGTCATCTATACTCTGCCTATGTTAACCATAAAATCAGACAAAGGCACTGGGGTTGTAACTTCAGTTCCATCAGATGCTCCTGATGACTATGCTGCTCTCagagatcttaaaaaaaaagaaccttttcgcaaaaagtataatataaCAGATGAAATGGTTTTGCCCTATGAACCAATCCCAATTATTGAAGTACCTGAACTTGGTAATCTTCCTGCCATTGTTGCTTGTGATATGTTTAAAGTAAACAGCCAAAATGACACTAAGCAACTGGCTGATGCAAAAGAACTAACttacaaaaaaggtttttatgaTGGTATTATGCTGGTTGAAGATTACAAAAACCAGAGAGTGCAAGATGTTAAGAAACttgtacaaaataaaatgttcgaagagGGTacagctttaaaatatttagagccagaaaaaaaagttgtatcaaGATCTGGTGATGAATGCATTGTAGCACTTTGTGACCAgtgGTATTTAGATTATGGTGAAGAAGAGTGgaagaataaaacaaaagaattgttGAATCGTTTAGAGACATTTTCAGATGAAACAAAGCATAACTTTGTGGCAACACTAGAATGGTTACATGAGCATGCATGTTCTCGCTCATATGGTTtagGCAGTAAAATTCCTTgggatgaaaaatatttaatagaatCTCTATCTGATTCTACAATTTACATGGCATACTATACTGTAGCTCATTTACTCCAGGGTGGTCAGATAAATGGATCAGTTGTTGGACCGTCTAATATAAGAGCAGACCAACTTACAGAAGAAGTTTGggattacatattttttaaagattgtcCTATTCCTTCCAGTACACAAATTGATCCAGATAATCTTAAAAAACTACAGCAAGAGTTTGAATATTGGTATCCACTGGACTTGCGTGTTTCTGGGAAAGATTTAATCCCTAATCATCTAACTTATTTCTTATACAATCATGTTGCTGTCTGGGCTAACCAACAAGAAAAATGGCCTAAGAGTGTACGAGCTAATGGtcatcttcttttaaattctgagAAAATGTCTAAATCTACTGGCAATTTCTTGACATTAGAGCATGCAATCAAAAAGTTCTCCGCTGatgGTATGAGGCTTGCACTTGCAGATGCTGGAGATTCTATTGAAGAtgcaaattttgttgaaaagacTGCTGATGCTGCTATACTAAGATTGTTTACCTTAGTAGAATGGACAAAGGAAATGATAGAAAATCAAGACAGCTTGAGATCAGGTTCACTTAACAATTTCAATGACAAAGTTTTCCAGCatgaaatgtACTTGGCAATCAATAAAGCTGAGAAAGcgtttgaaaaattattattcagGGAAGCTCtgaaagttgctttttttgaattgcaaGTCTCTCGTGATAAATACAGAGAGCTCTCACTAGATAAAATGCACAAAGACCTTGTTCTTAAATACATTGAGattcAGGCTTTGTTATTGTCACCGATTTGTCCGCACATATGCGAACATATTTGGCATCTTCTAGGAAAgGATGGAAGCATTTTAAATGCATCTTGGCCAGAATCTGCGGAAGTTGACAATAGTTTGTTAACATCATCACAATATTTAATGGATTCTAGTCGTGAATTTCGCTTAAgactaaaaaatatgttaactaCTCGAAAGAAAGGAAGTCATGACCTAGCGAAGCCCAATAGTGCTGTTGTTTACGTTGCAAAAGAGTATCCCCCATGGCAAAAAGCCGTGTTGGTTACACTTCGGAAATTATATGAGGCAAATAACAACGCTTTCCCAGATAACAAGGAAGTTATGGCCCTCTTTAAAGATGATgaactgattaaaaaacacatGAAGAAACTCATGCCTTTCGTTGCCTATGTCAAGGAGCGTGTACTCAAAGAAGGTATTTCAGCAATGGATCTCACTGTTCCGTTTGACGAAACCGCTGTACTTTGCGAAAATTTGGCTTATTTACTTAAATCGATTGAGttggAAAAGATAGACATTAAACCGTCTTCTGAAGCGGAACCTAAGATTCAAGAGGAGTGCCTTCCTGGAAGACCTTATTCTGTGTTtgtaatcaattaa

Transcript

BRAKERKRET00000001227

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5R614	Leucine--tRNA ligase, cytoplasmic OS=Pongo abelii OX=9601 GN=LARS1 PE=2 SV=1
Q9P2J5	Leucine--tRNA ligase, cytoplasmic OS=Homo sapiens OX=9606 GN=LARS1 PE=1 SV=2
Q8BMJ2	Leucine--tRNA ligase, cytoplasmic OS=Mus musculus OX=10090 GN=Lars1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002125 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
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
IPR004493 all species →	Family	Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR013155 all species →	Domain	Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding	Interproscan
IPR009008 all species →	Homologous_superfamily	Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain	Interproscan
IPR002300 all species →	Domain	Aminoacyl-tRNA synthetase, class Ia	Interproscan
IPR009080 all species →	Homologous_superfamily	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45794 all species →	LEUCYL-TRNA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0004823 all species →	Molecular Function	leucine-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006429 all species →	Biological Process	leucyl-tRNA aminoacylation	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	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
K01869	LARS, leuS; leucyl-tRNA synthetase	EC:6.1.1.4	Mitochondrial biogenesis	ko03029	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000001227.1 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

11TPM > 0

7Conditions

4.9Max TPM

0.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	3	0.42	4.86
Whole	6	5	0.56	0.92
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	0.45	0.45
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	0.74	0.74
symbioic hydra M9 strain · symbioic hydra rep1	1	1	0.29	0.29
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 / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	4.86
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	1.62
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	1.16
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	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
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
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
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.92
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	0.79
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	0.64
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	0.52
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	0.47
SRR10058802	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	0.45
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.74
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.29
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.