Gene detail

Detailed information of OS493_030712-T1 in Lophelia pertusa

Genomic Location: scaffold_201:339801...346412
NR annotation: KAJ7377117.1, 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
Q9P2J5	Leucine--tRNA ligase, cytoplasmic OS=Homo sapiens OX=9606 GN=LARS1 PE=1 SV=2
Q5R614	Leucine--tRNA ligase, cytoplasmic OS=Pongo abelii OX=9601 GN=LARS1 PE=2 SV=1
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)	OG0002117 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for OS493_030712-T1 in Lophelia pertusa.

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

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

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_030712-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_030712-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

109TPM > 0

7Conditions

44.6Max TPM

16.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.73	23.09
polyp at pH7 6	18	18	11.83	21.55
coral polyp · control treatment	16	16	23.04	44.64
coral polyp · oil and dispersant treatment	16	16	19.79	36.79
coral polyp · oil treatment	16	16	14.02	27.76
coral polyp · dispersant treatment	16	16	23.32	40.66
Polyp	10	9	6.41	14.95

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	-	23.09
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.68
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.93
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.01
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.75
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.64
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.63
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.34
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.42
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.75
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.17
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.17
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.82
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.12
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.57
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.55
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.12
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.79
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.04
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.93
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.29
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.89
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.85
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.89
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.92
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.90
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.48
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.10
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.91
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.23
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.33
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.64
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.12
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.45
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.46
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.53
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.40
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.45
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.08
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.04
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.29
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.25
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.45
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.94
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.85
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.76
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.79
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.57
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.86
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.80
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.53
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.73
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.40
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.20
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.71
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.18
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.68
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.34
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.42
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.27
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.66
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.76
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.59
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.41
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.77
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.99
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.80
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.20
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.11
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.17
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.13
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.57
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.91
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.87
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.47
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.42
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.66
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.20
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.73
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.29
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.97
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.61
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.93
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.42
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.15
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.92
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.35
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.63
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.94
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.41
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.90
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.95
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	8.17
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.56
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.44
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.28
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.39
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.87
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.64
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.78
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.