Gene detail

Detailed information of OS493_002574-T1 in Lophelia pertusa

Genomic Location: scaffold_5:4723945...4738519
NR annotation: KAJ7365853.1, hypothetical protein OS493_002574 [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
Q5U2U0	ATP-dependent clpX-like chaperone, mitochondrial OS=Rattus norvegicus OX=10116 GN=Clpx PE=2 SV=1
Q9JHS4	ATP-dependent clpX-like chaperone, mitochondrial OS=Mus musculus OX=10090 GN=Clpx PE=1 SV=2
O76031	ATP-dependent clpX-like chaperone, mitochondrial OS=Homo sapiens OX=9606 GN=CLPX PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004296 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07724 all species →	AAA_2	AAA domain (Cdc48 subfamily)	Domain	Interproscan
PF10431 all species →	ClpB_D2-small	C-terminal, D2-small domain, of ClpB protein	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019489 all species →	Domain	Clp ATPase, C-terminal	Interproscan
IPR003959 all species →	Domain	ATPase, AAA-type, core	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR050052 all species →	Family	ATP-dependent Clp protease ATP-binding subunit ClpX	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR004487 all species →	Family	Clp protease, ATP-binding subunit ClpX	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48102 all species →	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0005759 all species →	Cellular Component	mitochondrial matrix	Interproscan
GO:0051603 all species →	Biological Process	proteolysis involved in protein catabolic process	Interproscan
GO:0006457 all species →	Biological Process	protein folding	Interproscan
GO:0051082 all species →	Molecular Function	unfolded protein binding	Interproscan
GO:0140662 all species →	Molecular Function	ATP-dependent protein folding chaperone	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
K03544	clpX, CLPX; ATP-dependent Clp protease ATP-binding subunit ClpX	-	Chaperones and folding catalysts	ko03110	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_002574-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

182.9Max TPM

76.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	68.61	104.12
polyp at pH7 6	18	18	78.96	110.50
coral polyp · control treatment	16	16	74.45	122.39
coral polyp · oil and dispersant treatment	16	16	100.84	144.85
coral polyp · oil treatment	16	16	73.53	101.43
coral polyp · dispersant treatment	16	16	73.01	182.85
Polyp	10	10	64.07	113.98

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	104.12
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	101.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	93.03
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	91.65
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.16
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	74.08
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	73.26
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.44
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.75
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	67.48
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.60
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.48
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.16
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.08
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.35
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.97
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.56
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.42
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.50
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	109.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	95.87
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	93.02
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	90.14
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	89.30
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.78
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	83.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	83.07
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	82.55
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.92
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.59
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.98
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.18
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.96
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.32
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.90
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.73
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	122.39
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	121.45
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.69
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.23
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.88
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.28
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.65
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.95
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.72
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.35
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.07
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.95
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.72
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.60
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.36
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	144.85
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	143.31
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	117.71
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	116.03
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	108.79
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	104.53
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	102.61
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	100.89
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	98.16
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.31
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.83
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.40
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.05
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.92
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.66
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.45
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	101.43
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	100.93
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	88.38
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	87.43
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	86.93
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.86
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.16
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.50
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	74.60
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.94
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.94
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.89
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.86
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.04
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.34
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.25
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	182.85
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.63
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	86.01
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.60
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.54
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.68
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.61
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.81
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.31
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.33
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.70
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.39
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.12
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.60
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.56
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	113.98
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	97.19
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	88.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	77.67
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	64.80
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	54.97
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	42.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	35.75
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	34.72
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	31.41

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.