Gene detail

Detailed information of OS493_016240-T1 in Lophelia pertusa

Genomic Location: scaffold_49:2079112...2082049
NR annotation: KAJ7391935.1, 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
O60294	tRNA wybutosine-synthesizing protein 4 OS=Homo sapiens OX=9606 GN=LCMT2 PE=1 SV=3
Q8VY08	Leucine carboxyl methyltransferase 1 homolog OS=Arabidopsis thaliana OX=3702 GN=LCMT1 PE=1 SV=1
Q5XIA3	tRNA wybutosine-synthesizing protein 4 OS=Rattus norvegicus OX=10116 GN=Lcmt2 PE=2 SV=1

Gene family

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

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04072 all species →	LCM	Leucine carboxyl methyltransferase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR007213 all species →	Family	Methyltransferase Ppm1/Ppm2/Tcmp	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0032259 all species →	Biological Process	methylation	Interproscan
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

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_016240-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_016240-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

81TPM > 0

7Conditions

4.4Max TPM

1.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	9	0.72	3.04
polyp at pH7 6	18	8	0.47	1.69
coral polyp · control treatment	16	15	1.59	4.43
coral polyp · oil and dispersant treatment	16	13	1.04	2.49
coral polyp · oil treatment	16	15	1.77	3.98
coral polyp · dispersant treatment	16	13	1.16	3.48
Polyp	10	8	0.72	2.36

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.04
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.30
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.57
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.27
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.11
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.00
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.93
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.83
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.69
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.56
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.50
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.07
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.95
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.83
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.83
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.07
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.43
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.06
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.10
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.07
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.04
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.94
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.58
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.51
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.01
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.93
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.88
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.62
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.60
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.49
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.19
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.60
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.46
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.41
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.93
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.38
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.38
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.98
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.43
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.40
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.34
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.78
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.63
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.57
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.47
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.37
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.30
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.74
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.17
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.48
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.10
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.11
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.02
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.61
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.60
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.18
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.92
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.82
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.46
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.32
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.09
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.36
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.23
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.94
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.71
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.25
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.24
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.04
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.