Gene detail

Detailed information of OS493_002374-T1 in Lophelia pertusa

Genomic Location: scaffold_5:1311205...1316389
NR annotation: KAJ7365662.1, Glycine--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
P41250	Glycine--tRNA ligase OS=Homo sapiens OX=9606 GN=GARS1 PE=1 SV=3
Q5RBL1	Glycine--tRNA ligase OS=Pongo abelii OX=9601 GN=GARS1 PE=2 SV=1
Q5I0G4	Glycine--tRNA ligase OS=Rattus norvegicus OX=10116 GN=Gars1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004597 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03129 all species →	HGTP_anticodon	Anticodon binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036621 all species →	Homologous_superfamily	Anticodon-binding domain superfamily	Interproscan
IPR027031 all species →	Family	Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2	Interproscan
IPR045864 all species →	Homologous_superfamily	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Interproscan
IPR004154 all species →	Domain	Anticodon-binding	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10745 all species →	GLYCYL-TRNA SYNTHETASE/DNA POLYMERASE SUBUNIT GAMMA-2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004820 all species →	Molecular Function	glycine-tRNA ligase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006426 all species →	Biological Process	glycyl-tRNA aminoacylation	Interproscan
GO:0070150 all species →	Biological Process	mitochondrial glycyl-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_002374-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_002374-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

210.5Max TPM

34.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	38.05	57.54
polyp at pH7 6	18	18	38.49	68.33
coral polyp · control treatment	16	16	39.10	146.85
coral polyp · oil and dispersant treatment	16	16	22.62	67.20
coral polyp · oil treatment	16	16	33.22	81.68
coral polyp · dispersant treatment	16	16	23.47	82.79
Polyp	10	10	55.33	210.55

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	-	57.54
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.57
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.18
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.24
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.17
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.88
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.93
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.64
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.89
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.62
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.05
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.45
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.01
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.11
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.82
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.71
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.42
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.33
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.56
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.49
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.34
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.65
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.44
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.50
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.22
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.36
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.56
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.31
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.66
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.15
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.51
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.00
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	146.85
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.84
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.06
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.89
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.26
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.27
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.09
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.01
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.11
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.44
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.53
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.52
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.83
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.77
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.55
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.51
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.20
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.21
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.60
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.64
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.43
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.34
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.12
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.14
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.88
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.65
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.11
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.97
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.22
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.17
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.09
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	81.68
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.99
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.30
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.16
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.50
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.62
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.67
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.18
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.11
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.80
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.25
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.56
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.78
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.39
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.02
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.79
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.11
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.18
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.49
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.45
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.01
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.33
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.70
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.18
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.91
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.24
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.27
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.22
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.11
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.20
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.39
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	210.55
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	68.82
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	56.26
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	49.54
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	49.14
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	37.58
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	32.15
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	28.19
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.44
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.68

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.