Gene detail

Detailed information of OS493_001217-T1 in Lophelia pertusa

Genomic Location: scaffold_2:6507754...6519753
NR annotation: KAJ7387869.1, Cysteine--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
Q5F408	Cysteine--tRNA ligase, cytoplasmic OS=Gallus gallus OX=9031 GN=CARS1 PE=2 SV=1
Q4R550	Cysteine--tRNA ligase, cytoplasmic OS=Macaca fascicularis OX=9541 GN=CARS1 PE=2 SV=1
P49589	Cysteine--tRNA ligase, cytoplasmic OS=Homo sapiens OX=9606 GN=CARS1 PE=1 SV=3

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
IPR032678 all species →	Domain	tRNA synthetases class I, catalytic domain	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	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_001217-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_001217-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

28.3Max TPM

11.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.89	10.14
polyp at pH7 6	18	18	9.81	15.48
coral polyp · control treatment	16	16	13.10	28.28
coral polyp · oil and dispersant treatment	16	16	15.81	27.28
coral polyp · oil treatment	16	16	11.68	23.34
coral polyp · dispersant treatment	16	16	12.38	21.85
Polyp	10	10	7.77	13.57

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	-	10.14
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.62
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.14
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.91
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.70
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.48
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.39
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.22
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.11
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.99
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.68
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.52
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.46
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.39
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.92
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.02
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.75
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.63
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.48
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.86
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.45
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.35
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.13
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.59
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.25
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.26
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.57
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.54
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.47
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.40
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.24
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.69
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.59
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.22
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.71
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.73
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.28
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.92
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.72
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.34
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.09
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.48
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.10
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.91
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.50
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.46
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.33
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.55
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.81
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.97
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.28
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.60
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.24
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.03
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.97
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.83
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.60
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.60
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.16
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.83
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.28
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.51
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.01
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.93
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.63
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.34
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.91
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.75
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.48
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.92
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.43
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.26
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.56
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.80
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.79
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.76
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.28
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.74
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.85
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.79
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.42
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.29
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.63
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.24
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.87
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.55
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.12
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.86
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.78
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.64
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.63
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.03
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	13.57
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	13.39
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.25
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.07
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.76
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.76
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.68
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.62
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.61

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.