Gene detail

Detailed information of OS493_024515-T1 in Lophelia pertusa

Genomic Location: scaffold_114:1070190...1082079
NR annotation: KAJ7328594.1, hypothetical protein OS493_024515 [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
B3CQD1	Peptide chain release factor 1 OS=Orientia tsutsugamushi (strain Ikeda) OX=334380 GN=prfA PE=3 SV=1
A5CCS8	Peptide chain release factor 1 OS=Orientia tsutsugamushi (strain Boryong) OX=357244 GN=prfA PE=3 SV=1
Q67TD5	Peptide chain release factor 1 OS=Symbiobacterium thermophilum (strain DSM 24528 / JCM 14929 / IAM 14863 / T) OX=292459 GN=prfA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002637 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00472 all species →	RF-1	RF-1 domain	Family	Interproscan
PF03462 all species →	PCRF	PCRF domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000352 all species →	Domain	Peptide chain release factor class I	Interproscan
IPR045853 all species →	Homologous_superfamily	Peptide chain release factor class I superfamily	Interproscan
IPR050057 all species →	Family	Prokaryotic/Mitochondrial Release Factor	Interproscan
IPR005139 all species →	Domain	Peptide chain release factor	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43804 all species →	LD18447P	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003747 all species →	Molecular Function	translation release factor activity	Interproscan
GO:0006415 all species →	Biological Process	translational termination	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
K02835	prfA, MTRF1, MRF1; peptide chain release factor 1	-	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_024515-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

108TPM > 0

7Conditions

17.9Max TPM

4.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5.03	9.95
polyp at pH7 6	18	18	5.81	14.19
coral polyp · control treatment	16	16	6.41	17.95
coral polyp · oil and dispersant treatment	16	16	4.36	8.19
coral polyp · oil treatment	16	16	5.17	10.62
coral polyp · dispersant treatment	16	15	4.16	10.86
Polyp	10	9	2.66	5.83

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	-	9.95
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.78
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.24
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.19
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.55
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.48
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.28
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.23
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.22
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.07
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.92
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.68
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.62
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.40
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.98
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.86
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.66
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.19
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.67
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.42
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.39
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.99
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.83
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.16
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.04
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.71
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.62
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.13
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.64
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.57
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.85
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.45
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.41
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.33
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.15
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.95
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.82
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.64
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.76
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.30
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.02
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.90
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.81
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.21
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.30
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.46
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.10
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.94
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.09
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.49
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.19
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.89
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.06
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.75
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.05
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.86
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.65
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.12
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.95
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.85
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.35
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.33
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.32
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.64
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.63
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.08
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.62
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.21
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.30
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.93
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.50
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.01
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.76
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.33
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.30
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.92
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.47
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.20
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.63
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.42
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.61
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.86
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.80
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.05
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.83
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.78
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.82
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.25
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.23
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.08
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.87
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.61
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.37
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.83
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.56
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.96
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.71
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.36
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.20
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.75
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.74
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.43
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.