Gene detail

Detailed information of OS493_004869-T1 in Lophelia pertusa

Genomic Location: scaffold_10:428634...441265
NR annotation: KAJ7374531.1, Lysine--tRNA ligase [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

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
IPR006195 all species →	Domain	Aminoacyl-tRNA synthetase, class II	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
IPR018149 all species →	Domain	Lysyl-tRNA synthetase, class II, C-terminal	Interproscan
IPR004364 all species →	Domain	Aminoacyl-tRNA synthetase, class II (D/K/N)	Interproscan
IPR002313 all species →	Family	Lysine-tRNA ligase, class II	Interproscan
IPR045864 all species →	Homologous_superfamily	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	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:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0004824 all species →	Molecular Function	lysine-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006430 all species →	Biological Process	lysyl-tRNA aminoacylation	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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:0000049 all species →	Molecular Function	tRNA binding	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0017101 all species →	Cellular Component	aminoacyl-tRNA synthetase multienzyme complex	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 OS493_004869-T1 across 110 RNA-seq samples of Lophelia pertusa. 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.

110Samples

110TPM > 0

7Conditions

79.0Max TPM

37.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	28.74	43.42
polyp at pH7 6	18	18	36.04	67.54
coral polyp · control treatment	16	16	43.20	70.30
coral polyp · oil and dispersant treatment	16	16	46.52	78.96
coral polyp · oil treatment	16	16	37.68	66.22
coral polyp · dispersant treatment	16	16	34.45	66.27
Polyp	10	10	34.49	71.97

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.42
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.97
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.46
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.80
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.52
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.73
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.10
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.08
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.37
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.75
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.38
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.19
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.51
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.47
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.34
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.72
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.99
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.54
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.54
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.70
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.72
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.56
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.38
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.76
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.22
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.34
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.46
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.55
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.68
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.44
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.24
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.10
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.58
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.29
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.35
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.87
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.30
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.47
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.20
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.36
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.24
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.74
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.85
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.90
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.71
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.09
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.15
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.43
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.27
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.12
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.39
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.04
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.96
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.68
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.32
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.28
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.80
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.88
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.90
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.53
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.61
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.80
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.21
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.76
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.41
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.97
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.15
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.22
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.72
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.29
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.46
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.91
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.92
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.69
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.95
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.11
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.07
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.36
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.33
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.44
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.27
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.63
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.82
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.83
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.75
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.87
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.27
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.03
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.12
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.32
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.94
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.86
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.20
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.18
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	71.97
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	55.42
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	46.48
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	38.54
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	33.29
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	25.26
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	24.63
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	21.24
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.88
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.22

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 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.