Gene detail

Detailed information of OS493_022790-T1 in Lophelia pertusa

Genomic Location: scaffold_97:325347...353262
NR annotation: KAJ7390711.1, tRNA methyltransferase 1 [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
Q9NXH9	tRNA (guanine(26)-N(2))-dimethyltransferase OS=Homo sapiens OX=9606 GN=TRMT1 PE=1 SV=1
Q3TX08	tRNA (guanine(26)-N(2))-dimethyltransferase OS=Mus musculus OX=10090 GN=Trmt1 PE=1 SV=3
Q9VK89	tRNA (guanine(26)-N(2))-dimethyltransferase OS=Drosophila melanogaster OX=7227 GN=Trm1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005103 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02005 all species →	TRM	N2,N2-dimethylguanosine tRNA methyltransferase	Family	Interproscan
PF00642 all species →	zf-CCCH	Zinc finger C-x8-C-x5-C-x3-H type (and similar)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002905 all species →	Family	tRNA methyltransferase, Trm1	Interproscan
IPR000571 all species →	Domain	Zinc finger, CCCH-type	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR042296 all species →	Homologous_superfamily	tRNA methyltransferase, Trm1, C-terminal	Interproscan
IPR036855 all species →	Homologous_superfamily	Zinc finger, CCCH-type superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10631 all species →	N 2 ,N 2 -DIMETHYLGUANOSINE TRNA METHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0008033 all species →	Biological Process	tRNA processing	Interproscan
GO:0160102 all species →	Molecular Function	tRNA (guanine(10)-N2)-methyltransferase activity	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0002940 all species →	Biological Process	tRNA N2-guanine methylation	Interproscan
GO:0004809 all species →	Molecular Function	obsolete tRNA (guanine-N2-)-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
K00555	TRMT1, trm1; tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase	EC:2.1.1.215 EC:2.1.1.216	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_022790-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

24.1Max TPM

9.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.00	16.18
polyp at pH7 6	18	18	8.98	14.00
coral polyp · control treatment	16	16	11.71	24.15
coral polyp · oil and dispersant treatment	16	16	8.89	12.47
coral polyp · oil treatment	16	16	10.24	14.63
coral polyp · dispersant treatment	16	16	8.62	16.29
Polyp	10	10	4.29	7.24

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.18
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.60
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.81
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.60
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.85
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.11
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.32
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.84
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.44
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.63
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.86
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.64
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.50
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.03
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.47
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.46
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.23
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.96
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.90
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.84
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.78
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.22
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.75
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.65
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.28
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.10
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.68
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.26
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.24
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.14
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.42
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.15
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.56
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.89
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.24
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.75
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.60
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.92
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.08
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.96
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.79
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.79
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.31
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.39
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.31
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.45
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.14
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.47
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.99
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.56
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.03
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.64
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.87
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.66
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.57
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.38
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.12
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.66
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.94
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.85
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.84
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.35
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.26
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.63
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.59
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.77
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.76
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.61
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.02
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.34
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.77
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.00
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.59
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.56
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.02
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.80
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.29
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.98
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.95
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.67
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.24
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.20
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.69
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.32
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.22
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.84
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.71
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.66
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.66
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.37
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.83
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.24
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.11
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.16
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.04
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.90
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.55
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.15
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.14
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.59

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.