Gene detail

Detailed information of OS493_003742-T1 in Lophelia pertusa

Genomic Location: scaffold_7:5467089...5471006
NR annotation: KAJ7394068.1, Tar (HIV-1) RNA binding protein 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
Q13395	tRNA (guanosine(18)-2'-O)-methyltransferase TARBP1 OS=Homo sapiens OX=9606 GN=TARBP1 PE=1 SV=1
E9Q368	tRNA (guanosine(18)-2'-O)-methyltransferase TARBP1 OS=Mus musculus OX=10090 GN=Tarbp1 PE=1 SV=1
Q07527	tRNA (guanosine(18)-2'-O)-methyltransferase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TRM3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005153 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00588 all species →	SpoU_methylase	SpoU rRNA Methylase family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045330 all species →	Family	Probable methyltransferase Trm3/TARBP1	Interproscan
IPR001537 all species →	Domain	tRNA/rRNA methyltransferase, SpoU type	Interproscan
IPR044748 all species →	Domain	Trm3/ TARBP1, C-terminal	Interproscan
IPR029026 all species →	Homologous_superfamily	tRNA (guanine-N1-)-methyltransferase, N-terminal	Interproscan
IPR029028 all species →	Homologous_superfamily	Alpha/beta knot methyltransferases	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12029 all species →	RNA METHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016423 all species →	Molecular Function	tRNA (guanine) methyltransferase activity	Interproscan
GO:0030488 all species →	Biological Process	tRNA methylation	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0008173 all species →	Molecular Function	RNA methyltransferase activity	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_003742-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_003742-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

12.2Max TPM

3.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.59	6.93
polyp at pH7 6	18	18	4.85	9.81
coral polyp · control treatment	16	16	4.14	11.43
coral polyp · oil and dispersant treatment	16	16	2.63	5.98
coral polyp · oil treatment	16	16	3.19	5.31
coral polyp · dispersant treatment	16	16	2.41	9.35
Polyp	10	10	3.80	12.17

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.93
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.89
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.49
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.31
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.19
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.07
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.93
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.89
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.82
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.43
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.41
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.41
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.98
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.79
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.70
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.03
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.73
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.61
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.81
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.92
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.02
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.44
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.97
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.77
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.46
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.34
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.09
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.75
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.34
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.14
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.95
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.91
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.80
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.71
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.91
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.90
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.43
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.77
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.70
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.50
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.85
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.53
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.79
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.16
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.87
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.69
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.24
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.14
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.99
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.98
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.53
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.49
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.92
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.52
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.51
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.21
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.98
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.95
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.80
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.27
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.25
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.25
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.86
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.97
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.43
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.97
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.75
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.58
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.57
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.18
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.07
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.33
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.29
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.13
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.11
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.92
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.80
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.35
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.09
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.72
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.31
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.68
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.42
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.19
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.14
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.72
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.64
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	12.17
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.01
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.57
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.30
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.13
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.11
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.88
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.82
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.63
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.41

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.