Gene detail

Detailed information of OS493_033898-T1 in Lophelia pertusa

Genomic Location: scaffold_276:456198...463360
NR annotation: KAJ7321790.1, Tyrosine--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
Q6TGS6	Tyrosine--tRNA ligase, cytoplasmic OS=Danio rerio OX=7955 GN=yars1 PE=2 SV=2
Q5ZJ08	Tyrosine--tRNA ligase, cytoplasmic OS=Gallus gallus OX=9031 GN=YARS1 PE=2 SV=1
P54577	Tyrosine--tRNA ligase, cytoplasmic OS=Homo sapiens OX=9606 GN=YARS1 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001647 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00579 all species →	tRNA-synt_1b	tRNA synthetases class I (W and Y)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR023617 all species →	Family	Tyrosine-tRNA ligase, archaeal/eukaryotic-type	Interproscan
IPR050489 all species →	Family	Tyrosine--tRNA ligase	Interproscan
IPR002307 all species →	Family	Tyrosine-tRNA ligase	Interproscan
IPR002305 all species →	Family	Aminoacyl-tRNA synthetase, class Ic	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46264 all species →	TYROSINE-TRNA LIGASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004831 all species →	Molecular Function	tyrosine-tRNA ligase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006437 all species →	Biological Process	tyrosyl-tRNA aminoacylation	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0006418 all species →	Biological Process	tRNA aminoacylation for protein translation	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_033898-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_033898-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

49.3Max TPM

22.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.10	18.21
polyp at pH7 6	18	17	19.40	33.09
coral polyp · control treatment	16	16	29.08	43.53
coral polyp · oil and dispersant treatment	16	16	30.15	49.30
coral polyp · oil treatment	16	16	24.97	46.76
coral polyp · dispersant treatment	16	16	29.52	43.10
Polyp	10	10	11.76	19.69

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.48
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.10
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.29
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.13
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.99
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.63
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.31
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.30
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.85
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.98
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.40
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.89
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.81
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.87
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.66
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.89
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.09
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.53
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.42
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.68
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.82
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.73
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.40
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.07
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.80
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.55
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.13
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.64
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.09
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.53
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.54
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.85
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.32
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.35
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.02
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.81
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.01
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.96
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.76
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.80
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.35
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.14
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.88
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.80
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.19
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.30
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.20
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.51
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.82
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.80
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.45
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.33
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.53
SRR16705993	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	26.56
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.11
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.36
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.21
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.01
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.95
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.64
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.76
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.47
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.90
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.64
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.22
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.79
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.23
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.50
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.61
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.34
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.29
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.25
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.10
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.04
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.03
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.10
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.97
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.27
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.25
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.98
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.30
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.86
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.81
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.76
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.45
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.93
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.25
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.19
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.78
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.61
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.69
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	19.09
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.73
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	12.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	10.28
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	9.93
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.08
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.52
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.17
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.67

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.