Gene detail

Detailed information of OS493_029776-T1 in Lophelia pertusa

Genomic Location: scaffold_184:291520...297720
NR annotation: KAJ7370786.1, hypothetical protein OS493_029776 [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
Q1JPX3	Phenylalanine--tRNA ligase alpha subunit OS=Danio rerio OX=7955 GN=farsa PE=2 SV=2
Q7SYV0	Phenylalanine--tRNA ligase alpha subunit B OS=Xenopus laevis OX=8355 GN=farsa-b PE=2 SV=1
Q6AZG6	Phenylalanine--tRNA ligase alpha subunit A OS=Xenopus laevis OX=8355 GN=farsa-a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004071 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18553 all species →	PheRS_DBD3	PheRS DNA binding domain 3	Domain	Interproscan
PF01409 all species →	tRNA-synt_2d	tRNA synthetases class II core domain (F)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR040725 all species →	Domain	PheRS, DNA binding domain 3	Interproscan
IPR006195 all species →	Domain	Aminoacyl-tRNA synthetase, class II	Interproscan
IPR004529 all species →	Family	Phenylalanyl-tRNA synthetase, class IIc, alpha subunit	Interproscan
IPR045864 all species →	Homologous_superfamily	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Interproscan
IPR002319 all species →	Domain	Phenylalanyl-tRNA synthetase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11538 all species →	PHENYLALANYL-TRNA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0004826 all species →	Molecular Function	phenylalanine-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006432 all species →	Biological Process	phenylalanyl-tRNA aminoacylation	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0009328 all species →	Cellular Component	phenylalanine-tRNA ligase complex	Interproscan
GO:0000049 all species →	Molecular Function	tRNA binding	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0043039 all species →	Biological Process	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K01889	FARSA, pheS; phenylalanyl-tRNA synthetase alpha chain	EC:6.1.1.20	Transfer RNA biogenesis	ko03016	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_029776-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

94.3Max TPM

40.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	40.45	61.70
polyp at pH7 6	18	18	45.20	59.62
coral polyp · control treatment	16	16	42.24	60.50
coral polyp · oil and dispersant treatment	16	16	39.03	57.20
coral polyp · oil treatment	16	16	40.60	57.29
coral polyp · dispersant treatment	16	16	29.99	45.22
Polyp	10	10	46.91	94.29

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.70
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.01
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.88
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.09
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.04
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.79
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.42
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.93
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.59
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.31
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.87
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.67
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.56
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.41
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.79
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.22
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.09
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.81
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.62
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.17
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.51
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.06
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.69
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.24
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.40
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.56
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.74
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.61
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.03
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.87
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.85
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.55
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.42
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.29
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.81
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.23
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.50
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.76
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.28
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.80
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.90
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.57
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.25
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.98
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.95
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.75
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.36
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.69
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.47
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.28
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.23
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.20
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.14
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.36
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.85
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.01
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.57
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.57
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.92
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.83
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.70
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.15
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.67
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.54
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.98
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.06
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.29
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.22
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.08
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.87
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.71
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.58
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.13
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.94
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.27
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.13
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.96
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.61
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.65
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.71
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.28
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.85
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.65
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.22
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.28
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.08
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.73
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.82
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.25
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.82
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.31
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.89
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	94.29
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	50.73
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	49.98
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	45.77
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	45.38
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	42.27
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	41.04
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	37.38
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	31.53
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	30.71

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.