Gene detail

Detailed information of OS493_016241-T1 in Lophelia pertusa

Genomic Location: scaffold_49:2082142...2089453
NR annotation: KAJ7391936.1, Leucine carboxyl methyltransferase 2 [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
Q5XIA3	tRNA wybutosine-synthesizing protein 4 OS=Rattus norvegicus OX=10116 GN=Lcmt2 PE=2 SV=1
Q8BYR1	tRNA wybutosine-synthesizing protein 4 OS=Mus musculus OX=10090 GN=Lcmt2 PE=2 SV=4
O60294	tRNA wybutosine-synthesizing protein 4 OS=Homo sapiens OX=9606 GN=LCMT2 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001733 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13418 all species →	Kelch_4	Galactose oxidase, central domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR015915 all species →	Homologous_superfamily	Kelch-type beta propeller	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46529 all species →	TRNA WYBUTOSINE-SYNTHESIZING PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008175 all species →	Molecular Function	tRNA methyltransferase activity	Interproscan
GO:0030488 all species →	Biological Process	tRNA methylation	Interproscan
GO:0031591 all species →	Biological Process	wybutosine biosynthetic process	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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_016241-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_016241-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

8.2Max TPM

2.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2.74	4.57
polyp at pH7 6	18	17	3.32	7.05
coral polyp · control treatment	16	16	2.48	4.25
coral polyp · oil and dispersant treatment	16	16	1.83	3.80
coral polyp · oil treatment	16	16	2.64	4.31
coral polyp · dispersant treatment	16	16	1.57	3.72
Polyp	10	10	2.28	8.19

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.57
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.92
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.32
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.23
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.22
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.21
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.06
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.68
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.52
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.50
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.50
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.42
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.19
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.63
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.60
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.55
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.05
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.53
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.53
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.21
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.05
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.95
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.71
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.17
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.12
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.03
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.75
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.13
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.08
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.02
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.38
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.08
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.25
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.13
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.37
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.21
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.13
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.87
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.66
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.65
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.64
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.53
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.79
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.47
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.45
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.37
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.32
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.88
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.80
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.61
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.74
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.34
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.20
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.13
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.91
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.89
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.46
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.35
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.22
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.20
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.87
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.85
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.76
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.31
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.90
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.50
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.39
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.35
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.13
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.08
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.95
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.34
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.13
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.05
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.74
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.73
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.71
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.72
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.66
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.41
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.06
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.96
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.68
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.42
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.82
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.72
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.59
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.52
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.35
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.13
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	8.19
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.67
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.22
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.99
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.88
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.72
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.66
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.07
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.87
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.50

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.