Gene detail

Detailed information of OS493_015717-T1 in Lophelia pertusa

Genomic Location: scaffold_47:2103425...2110961
NR annotation: KAJ7360609.1, Pachytene checkpoint protein 2 [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
Q15645	Pachytene checkpoint protein 2 homolog OS=Homo sapiens OX=9606 GN=TRIP13 PE=1 SV=2
D3K5L7	Pachytene checkpoint protein 2 homolog OS=Sus scrofa OX=9823 GN=TRIP13 PE=2 SV=1
E2R222	Pachytene checkpoint protein 2 homolog OS=Canis lupus familiaris OX=9615 GN=TRIP13 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005062 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00004 all species →	AAA	ATPase family associated with various cellular activities (AAA)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR044539 all species →	Family	Pachytene checkpoint protein 2-like	Interproscan
IPR001270 all species →	Family	ClpA/B family	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR003959 all species →	Domain	ATPase, AAA-type, core	Interproscan
IPR003960 all species →	Conserved_site	ATPase, AAA-type, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45991 all species →	PACHYTENE CHECKPOINT PROTEIN 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005694 all species →	Cellular Component	chromosome	Interproscan
GO:0007131 all species →	Biological Process	reciprocal meiotic recombination	Interproscan
GO:0051598 all species →	Biological Process	meiotic recombination checkpoint signaling	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis 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
K22399	TRIP13; pachytene checkpoint protein 2	-	Chromosome and associated proteins	ko03036	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_015717-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

88.3Max TPM

7.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.64	9.90
polyp at pH7 6	18	17	4.45	8.85
coral polyp · control treatment	16	16	13.40	88.28
coral polyp · oil and dispersant treatment	16	16	9.95	56.11
coral polyp · oil treatment	16	16	7.98	13.53
coral polyp · dispersant treatment	16	16	4.92	9.57
Polyp	10	10	5.57	14.29

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.90
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.78
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.17
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.09
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.80
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.77
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.55
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.49
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.99
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.81
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.51
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.96
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.84
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.48
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.17
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.12
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.89
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.85
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.37
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.12
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.53
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.50
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.49
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.88
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.43
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.22
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.98
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.58
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.37
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.25
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.92
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.91
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.64
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	88.28
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.98
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.41
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.02
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.73
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.13
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.23
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.23
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.83
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.69
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.60
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.36
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.97
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.30
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.36
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.11
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.28
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.12
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.49
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.78
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.11
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.08
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.06
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.85
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.73
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.29
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.88
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.41
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.33
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.36
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.34
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.53
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.27
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.60
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.19
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.89
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.12
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.69
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.64
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.62
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.61
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.39
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.18
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.99
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.32
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.94
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.57
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.16
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.12
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.07
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.41
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.91
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.16
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.18
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.95
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.61
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.31
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.24
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.81
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.37
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.24
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.29
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.47
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.74
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.92
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.66
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.53
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.47
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.07
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.38
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.15

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.