Gene detail

Detailed information of OS493_029323-T1 in Lophelia pertusa

Genomic Location: scaffold_177:356693...360455
NR annotation: KAJ7377423.1, hypothetical protein OS493_029323 [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
P49696	Valine--tRNA ligase OS=Takifugu rubripes OX=31033 GN=vars1 PE=3 SV=1
Q04462	Valine--tRNA ligase OS=Rattus norvegicus OX=10116 GN=Vars1 PE=2 SV=2
Q9Z1Q9	Valine--tRNA ligase OS=Mus musculus OX=10090 GN=Vars1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002985 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08264 all species →	Anticodon_1	Anticodon-binding domain of tRNA ligase	Domain	Interproscan
PF10458 all species →	Val_tRNA-synt_C	Valyl tRNA synthetase tRNA binding arm	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013155 all species →	Domain	Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding	Interproscan
IPR019499 all species →	Domain	Valyl-tRNA synthetase, tRNA-binding arm	Interproscan
IPR009080 all species →	Homologous_superfamily	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Interproscan
IPR002303 all species →	Family	Valine-tRNA ligase	Interproscan
IPR010978 all species →	Homologous_superfamily	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Interproscan
IPR037118 all species →	Homologous_superfamily	Valyl-tRNA synthetase, tRNA-binding arm superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11946 all species →	VALYL-TRNA SYNTHETASES	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0006418 all species →	Biological Process	tRNA aminoacylation for protein translation	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0004832 all species →	Molecular Function	valine-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006438 all species →	Biological Process	valyl-tRNA aminoacylation	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	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_029323-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_029323-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

241.6Max TPM

70.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	49.12	72.11
polyp at pH7 6	18	18	86.66	180.96
coral polyp · control treatment	16	16	79.57	241.64
coral polyp · oil and dispersant treatment	16	16	94.16	193.57
coral polyp · oil treatment	16	16	63.87	92.22
coral polyp · dispersant treatment	16	16	63.24	161.29
Polyp	10	10	53.43	104.61

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.11
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.38
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.95
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.44
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.38
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.98
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.34
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.13
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.49
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.30
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.30
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.72
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.22
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.71
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.83
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.19
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.40
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.22
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	180.96
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	170.60
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	112.63
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	106.80
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	105.48
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	86.34
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.49
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.18
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.19
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.96
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.25
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.72
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.42
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.02
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.34
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.42
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.10
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	241.64
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	117.24
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.15
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	104.46
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.25
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.25
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.72
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.10
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.47
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.26
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.04
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.70
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.93
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.84
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.13
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	193.57
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	192.22
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	122.61
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.97
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	102.30
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	92.62
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.22
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.56
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	83.78
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.49
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.91
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.34
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.60
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.47
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.03
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.92
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.22
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	81.02
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.60
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.20
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.24
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.27
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.19
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.50
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.08
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.05
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.47
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.53
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.90
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.41
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.80
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	161.29
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	134.43
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	86.60
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.42
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.56
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.42
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.66
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.24
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.46
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.57
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.09
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.05
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.47
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.77
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	104.61
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	87.43
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	75.20
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	73.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	51.74
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	44.11
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	31.88
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	28.07
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	21.13
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.62

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.