Gene detail

Detailed information of OS493_001216-T1 in Lophelia pertusa

Genomic Location: scaffold_2:6501394...6503300
NR annotation: KAJ7387868.1, hypothetical protein OS493_001216 [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
P49589	Cysteine--tRNA ligase, cytoplasmic OS=Homo sapiens OX=9606 GN=CARS1 PE=1 SV=3
Q4R550	Cysteine--tRNA ligase, cytoplasmic OS=Macaca fascicularis OX=9541 GN=CARS1 PE=2 SV=1
Q7ZWR2	Cysteine--tRNA ligase, cytoplasmic OS=Xenopus laevis OX=8355 GN=cars1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002418 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01406 all species →	tRNA-synt_1e	tRNA synthetases class I (C) catalytic domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR024909 all species →	Family	Cysteinyl-tRNA synthetase/mycothiol ligase	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR032678 all species →	Domain	tRNA synthetases class I, catalytic domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10890 all species →	CYSTEINYL-TRNA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004817 all species →	Molecular Function	cysteine-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006423 all species →	Biological Process	cysteinyl-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_001216-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_001216-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

68.0Max TPM

23.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	12.36	22.77
polyp at pH7 6	18	17	14.61	35.34
coral polyp · control treatment	16	16	31.64	67.99
coral polyp · oil and dispersant treatment	16	16	32.68	67.01
coral polyp · oil treatment	16	16	23.63	37.07
coral polyp · dispersant treatment	16	16	25.73	46.51
Polyp	10	10	27.31	49.09

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.77
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.44
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.72
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.80
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.38
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.32
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.45
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.89
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.52
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.74
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.65
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.43
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.25
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.08
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.87
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.44
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.17
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.34
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.17
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.63
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.40
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.87
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.94
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.20
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.49
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.77
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.06
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.61
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.15
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.13
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.12
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.05
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.99
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.06
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.81
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.29
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.86
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.81
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.37
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.27
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.99
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.54
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.86
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.10
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.83
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.53
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.86
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.01
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.22
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.17
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.23
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.91
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.45
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.24
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.81
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.01
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.81
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.83
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.29
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.99
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.11
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.07
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.57
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.54
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.12
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.37
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.22
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.98
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.10
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.90
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.36
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.01
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.52
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.21
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.34
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.25
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.51
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.97
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.71
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.61
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.11
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.62
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.88
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.35
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.76
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.19
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.58
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.07
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.95
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.26
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.06
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	49.09
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	32.88
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	32.26
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	30.81
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	30.08
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	27.41
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	20.43
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	20.04
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	19.26
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.82

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.