Gene detail

Detailed information of OS493_034717-T1 in Lophelia pertusa

Genomic Location: scaffold_297:352439...361066
NR annotation: KAJ7376440.1, ribosome biogenesis protein tsr3 [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
Q5HZH2	18S rRNA aminocarboxypropyltransferase OS=Mus musculus OX=10090 GN=Tsr3 PE=1 SV=1
Q9UJK0	18S rRNA aminocarboxypropyltransferase OS=Homo sapiens OX=9606 GN=TSR3 PE=1 SV=1
Q58118	16S rRNA aminocarboxypropyltransferase OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) OX=243232 GN=MJ0708 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0024579 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04034 all species →	Ribo_biogen_C	Ribosome biogenesis protein, C-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR022968 all species →	Family	16S/18S rRNA aminocarboxypropyltransferase Tsr3	Interproscan
IPR007177 all species →	Domain	16S/18S rRNA aminocarboxypropyltransferase Tsr3, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR20426 all species →	RIBOSOME BIOGENESIS PROTEIN TSR3 HOMOLOG	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006364 all species →	Biological Process	rRNA processing	Interproscan
GO:0016740 all species →	Molecular Function	transferase activity	Interproscan
GO:0030490 all species →	Biological Process	maturation of SSU-rRNA	Interproscan
GO:0106388 all species →	Molecular Function	18S rRNA aminocarboxypropyltransferase 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_034717-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_034717-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

23.4Max TPM

5.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.51	23.40
polyp at pH7 6	18	18	8.27	10.90
coral polyp · control treatment	16	16	4.01	6.76
coral polyp · oil and dispersant treatment	16	16	2.43	4.06
coral polyp · oil treatment	16	16	3.76	5.75
coral polyp · dispersant treatment	16	16	2.34	4.39
Polyp	10	10	5.76	8.77

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	-	23.40
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.15
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.03
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.30
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.46
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.38
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.97
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.23
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.18
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.09
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.70
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.41
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.19
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.19
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.82
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.67
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.38
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.71
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.90
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.41
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.96
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.66
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.66
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.59
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.29
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.32
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.27
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.19
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.19
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.78
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.52
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.96
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.65
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.87
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.55
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.76
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.62
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.42
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.06
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.00
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.80
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.33
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.32
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.03
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.82
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.81
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.86
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.81
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.50
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.17
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.85
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.62
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.57
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.30
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.29
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.02
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.97
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.69
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.14
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.64
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.53
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.34
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.76
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.56
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.75
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.49
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.25
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.13
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.84
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.29
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.07
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.77
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.43
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.35
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.20
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.89
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.85
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.67
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.86
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.36
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.39
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.66
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.32
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.06
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.99
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.88
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.45
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.06
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.87
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.78
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.72
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.54
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.20
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.77
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	8.58
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.79
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.55
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.98
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.01
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.98
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.14
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.56
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.19

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.