Gene detail

Detailed information of OS493_032937-T1 in Lophelia pertusa

Genomic Location: scaffold_252:64005...73290
NR annotation: KAJ7322756.1, tRNA (cytosine-5-)-methyltransferase [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
O55055	tRNA (cytosine(38)-C(5))-methyltransferase OS=Mus musculus OX=10090 GN=Trdmt1 PE=1 SV=2
O14717	tRNA (cytosine(38)-C(5))-methyltransferase OS=Homo sapiens OX=9606 GN=TRDMT1 PE=1 SV=1
Q7YS61	tRNA (cytosine(38)-C(5))-methyltransferase OS=Bos taurus OX=9913 GN=TRDMT1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004321 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00145 all species →	DNA_methylase	C-5 cytosine-specific DNA methylase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR001525 all species →	Family	C-5 cytosine methyltransferase	Interproscan
IPR031303 all species →	Conserved_site	DNA methylase, C-5 cytosine-specific, conserved site	Interproscan
IPR050750 all species →	Family	Cytosine-specific C5-methyltransferase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46098 all species →	TRNA (CYTOSINE(38)-C(5))-METHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K15336	TRDMT1, DNMT2; tRNA (cytosine38-C5)-methyltransferase	EC:2.1.1.204	Transfer RNA biogenesis	ko03016	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_032937-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

16.9Max TPM

3.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.68	6.72
polyp at pH7 6	18	18	4.56	7.04
coral polyp · control treatment	16	16	3.85	13.17
coral polyp · oil and dispersant treatment	16	16	2.68	16.90
coral polyp · oil treatment	16	16	3.16	7.73
coral polyp · dispersant treatment	16	16	1.87	4.40
Polyp	10	10	5.35	12.24

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.72
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.09
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.03
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.92
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.68
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.58
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.39
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.98
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.82
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.61
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.19
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.83
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.59
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.16
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.14
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.72
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.04
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.37
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.14
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.30
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.15
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.01
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.77
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.34
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.20
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.18
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.71
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.57
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.37
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.37
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.31
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.02
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.17
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.02
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.41
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.38
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.06
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.04
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.60
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.50
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.18
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.62
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.49
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.42
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.41
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.02
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.29
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.17
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.95
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.85
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.50
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.42
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.03
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.55
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.54
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.34
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.33
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.28
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.05
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.50
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.73
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.54
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.32
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.84
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.57
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.37
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.71
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.42
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.36
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.09
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.72
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.20
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.10
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.81
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.40
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.31
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.27
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.51
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.21
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.16
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.83
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.40
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.87
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.76
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.65
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.65
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.64
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.61
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.24
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.93
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.31
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.72
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.35
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.55
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.29
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.74
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.97
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.40

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.