Gene detail

Detailed information of OS493_030714-T1 in Lophelia pertusa

Genomic Location: scaffold_201:354856...364544
NR annotation: KAJ7377119.1, Leucine--tRNA ligase, cytoplasmic [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
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
PF09334 all species →	tRNA-synt_1g	tRNA synthetases class I (M)	Family	Interproscan
PF08264 all species →	Anticodon_1	Anticodon-binding domain of tRNA ligase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015413 all species →	Domain	Methionyl/Leucyl tRNA synthetase	Interproscan
IPR009080 all species →	Homologous_superfamily	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Interproscan
IPR004493 all species →	Family	Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic	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

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: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:0004823 all species →	Molecular Function	leucine-tRNA ligase activity	Interproscan
GO:0006429 all species →	Biological Process	leucyl-tRNA aminoacylation	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

No KEGG orthology assignment for OS493_030714-T1.

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_030714-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

93.3Max TPM

37.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	31.32	54.54
polyp at pH7 6	18	18	33.42	60.33
coral polyp · control treatment	16	16	49.45	93.34
coral polyp · oil and dispersant treatment	16	16	44.75	79.47
coral polyp · oil treatment	16	16	34.99	49.65
coral polyp · dispersant treatment	16	16	42.66	61.37
Polyp	10	10	19.22	41.44

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.54
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.95
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.72
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.98
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.93
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.55
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.98
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.80
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.37
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.77
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.20
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.85
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.35
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.39
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.53
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.90
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.33
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.49
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.29
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.24
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.97
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.39
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.93
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.19
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.75
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.13
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.02
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.25
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.89
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.46
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.17
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.32
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.34
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.41
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.17
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.81
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.24
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.12
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.77
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.13
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.18
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.83
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.32
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.79
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.54
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.80
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.47
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.79
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.20
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.60
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.15
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.04
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.55
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.53
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.30
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.29
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.16
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.38
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.10
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.45
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.22
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.65
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.98
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.79
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.13
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.72
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.99
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.06
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.44
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.09
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.70
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.70
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.18
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.94
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.27
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.95
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.25
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.95
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.04
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.86
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.17
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.54
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.52
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.69
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.59
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.97
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.57
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.81
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.48
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	41.44
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	22.09
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	21.94
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	21.41
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	20.89
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	20.30
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.59
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	10.08
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.30
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.13

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.