Gene detail

Detailed information of OS493_002232-T1 in Lophelia pertusa

Genomic Location: scaffold_4:7328747...7332672
NR annotation: KAJ7375459.1, peptidyl-tRNA hydrolase 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
Q8BW00	Probable peptidyl-tRNA hydrolase OS=Mus musculus OX=10090 GN=Ptrh1 PE=2 SV=1
Q86Y79	Peptidyl-tRNA hydrolase OS=Homo sapiens OX=9606 GN=PTRH1 PE=1 SV=1
Q88Z39	Peptidyl-tRNA hydrolase OS=Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) OX=220668 GN=pth PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007228 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01195 all species →	Pept_tRNA_hydro	Peptidyl-tRNA hydrolase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036416 all species →	Homologous_superfamily	Peptidyl-tRNA hydrolase superfamily	Interproscan
IPR001328 all species →	Family	Peptidyl-tRNA hydrolase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR17224 all species →	PEPTIDYL-TRNA HYDROLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004045 all species →	Molecular Function	aminoacyl-tRNA hydrolase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K01056	PTH1, PTRH1, pth, spoVC; peptidyl-tRNA hydrolase, PTH1 family	EC:3.1.1.29	Translation factors	ko03012	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_002232-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

109TPM > 0

7Conditions

41.2Max TPM

9.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.32	18.40
polyp at pH7 6	18	18	10.48	22.64
coral polyp · control treatment	16	16	10.86	41.22
coral polyp · oil and dispersant treatment	16	16	8.01	28.88
coral polyp · oil treatment	16	16	8.03	13.44
coral polyp · dispersant treatment	16	16	10.69	20.15
Polyp	10	9	6.30	10.65

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.40
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.78
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.26
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.00
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.55
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.15
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.49
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.13
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.57
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.46
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.39
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.19
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.83
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.72
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.31
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.28
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.26
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.64
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.31
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.48
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.44
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.26
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.41
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.94
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.92
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.90
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.39
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.94
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.41
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.38
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.32
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.23
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.86
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.75
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.98
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.22
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.96
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.66
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.63
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.57
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.33
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.32
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.17
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.65
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.54
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.87
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.81
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.42
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.76
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.58
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.88
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.31
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.03
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.13
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.79
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.68
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.85
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.27
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.16
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.09
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.66
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.30
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.09
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.08
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.92
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.44
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.21
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.23
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.07
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.64
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.29
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.81
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.70
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.61
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.25
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.56
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.66
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.06
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.15
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.62
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.75
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.56
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.61
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.21
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.49
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.40
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.32
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.48
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.11
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.55
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.35
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.03
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	10.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.91
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.57
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.21
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.75
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.22
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.93
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.76
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.05
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.