Gene detail

Detailed information of OS493_002371-T1 in Lophelia pertusa

Genomic Location: scaffold_5:1245502...1254553
NR annotation: KAJ7365659.1, 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
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
IPR036621 all species →	Homologous_superfamily	Anticodon-binding domain superfamily	Interproscan
IPR002315 all species →	Family	Glycyl-tRNA synthetase	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
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	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_002371-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_002371-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

206.9Max TPM

29.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	30.52	43.65
polyp at pH7 6	18	18	34.65	72.26
coral polyp · control treatment	16	16	33.07	116.23
coral polyp · oil and dispersant treatment	16	16	19.81	57.96
coral polyp · oil treatment	16	16	29.73	80.31
coral polyp · dispersant treatment	16	16	18.59	73.27
Polyp	10	10	46.14	206.87

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.65
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.47
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.79
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.48
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.15
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.65
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.58
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.30
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.15
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.61
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.90
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.50
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.58
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.12
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.33
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.12
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.83
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.22
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.26
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.22
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.67
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.50
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.82
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.03
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.01
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.59
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.30
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.70
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.72
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.65
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.66
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.42
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.64
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.31
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.19
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	116.23
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.26
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.84
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.28
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.29
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.28
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.25
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.25
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.66
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.86
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.43
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.09
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.49
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.96
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.56
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.39
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.47
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.50
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.82
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.86
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.79
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.18
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.64
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.99
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.81
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.07
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.71
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.58
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.69
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.31
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.97
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.85
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.30
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.92
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.15
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.62
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.44
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.12
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.77
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.90
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.31
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.45
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.32
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.93
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.27
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.46
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.61
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.55
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.38
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.58
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.73
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.58
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.57
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.67
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.62
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.58
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.54
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.85
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.92
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	206.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	65.07
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	51.53
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	45.94
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	25.09
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	23.01
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	19.76
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	11.20
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.79
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.14

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.