Gene detail

Detailed information of CAB3996964.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3996964.1, lysine--tRNA ligase isoform X2 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3996964.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q99MN1	Lysine--tRNA ligase OS=Mus musculus OX=10090 GN=Kars1 PE=1 SV=1
P37879	Lysine--tRNA ligase OS=Cricetulus griseus OX=10029 GN=KARS1 PE=1 SV=1
Q15046	Lysine--tRNA ligase OS=Homo sapiens OX=9606 GN=KARS1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003612 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01336 all species →	tRNA_anti-codon	OB-fold nucleic acid binding domain	Domain	Interproscan
PF00152 all species →	tRNA-synt_2	tRNA synthetases class II (D, K and N)	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
IPR006195 all species →	Domain	Aminoacyl-tRNA synthetase, class II	Interproscan
IPR018149 all species →	Domain	Lysyl-tRNA synthetase, class II, C-terminal	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR004365 all species →	Domain	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Interproscan
IPR034762 all species →	Family	Bacterial/eukaryotic lysine-tRNA ligase, class II	Interproscan
IPR004364 all species →	Domain	Aminoacyl-tRNA synthetase, class II (D/K/N)	Interproscan
IPR002313 all species →	Family	Lysine-tRNA ligase, class II	Interproscan
IPR044136 all species →	Domain	Lysine-tRNA ligase, class II, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR42918 all species →	LYSYL-TRNA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000049 all species →	Molecular Function	tRNA binding	Interproscan
GO:0004824 all species →	Molecular Function	lysine-tRNA ligase activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006430 all species →	Biological Process	lysyl-tRNA aminoacylation	Interproscan
GO:0017101 all species →	Cellular Component	aminoacyl-tRNA synthetase multienzyme complex	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	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
K04567	KARS, lysS; lysyl-tRNA synthetase, class II	EC:6.1.1.6	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 CAB3996964.1 across 21 RNA-seq samples of Paramuricea clavata. 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.

21Samples

18TPM > 0

4Conditions

105.9Max TPM

41.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	56.55	105.85
apical branchlet · Temperature treatment at T0	6	6	41.89	101.24
apical branchlet · Temperature treatment at T25	5	4	27.89	55.78
apical branchlet · Control at T0	4	3	36.40	101.66

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	105.85
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	92.92
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	64.15
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	51.25
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	25.13
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	101.24
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	50.30
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	37.82
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	28.90
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	21.57
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	11.50
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	55.78
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	35.80
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	35.46
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	12.42
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	101.66
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	36.13
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	7.83
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 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.