Gene detail

Detailed information of OS493_003109-T1 in Lophelia pertusa

Genomic Location: scaffold_6:5445590...5450729
NR annotation: KAJ7340365.1, Pentatricopeptide repeat-containing protein 1, mitochondrial [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
Q9LUC2	Pentatricopeptide repeat-containing protein At3g14730 OS=Arabidopsis thaliana OX=3702 GN=PCMP-E31 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009404 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13041 all species →	PPR_2	PPR repeat family	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002885 all species →	Repeat	Pentatricopeptide repeat	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR051240 all species →	Family	Mitochondrial RNA Processing and Respiration	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47933 all species →	PENTATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 1, MITOCHONDRIAL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	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_003109-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_003109-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

8.3Max TPM

3.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.13	5.75
polyp at pH7 6	18	18	3.93	5.94
coral polyp · control treatment	16	16	4.53	8.30
coral polyp · oil and dispersant treatment	16	16	3.03	4.83
coral polyp · oil treatment	16	16	3.79	6.81
coral polyp · dispersant treatment	16	16	2.50	5.42
Polyp	10	10	2.47	4.33

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.75
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.30
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.66
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.62
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.58
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.49
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.35
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.25
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.08
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.97
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.69
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.66
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.64
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.38
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.06
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.80
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.56
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.43
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.94
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.81
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.72
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.67
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.59
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.20
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.11
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.10
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.85
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.72
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.64
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.07
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.44
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.34
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.80
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.30
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.97
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.30
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.24
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.89
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.63
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.27
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.28
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.14
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.07
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.77
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.55
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.50
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.61
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.13
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.83
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.83
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.79
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.40
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.09
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.27
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.80
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.46
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.35
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.20
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.94
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.32
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.29
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.81
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.43
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.03
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.01
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.80
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.19
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.04
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.77
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.49
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.19
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.81
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.69
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.28
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.80
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.53
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.42
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.01
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.24
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.96
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.74
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.84
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.71
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.70
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.33
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.92
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.89
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.30
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.17
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.57
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.11
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.33
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.62
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.99
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.97
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.56
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.23
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.13
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.78
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.64
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.41

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.