Gene detail

Detailed information of OS493_003130-T1 in Lophelia pertusa

Genomic Location: scaffold_6:5603687...5608394
NR annotation: KAJ7340386.1, AP endonuclease 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
Q5LG28	Probable endonuclease 4 OS=Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2) OX=272559 GN=nfo PE=3 SV=1
Q64WY5	Probable endonuclease 4 OS=Bacteroides fragilis (strain YCH46) OX=295405 GN=nfo PE=3 SV=1
Q89YT0	Probable endonuclease 4 OS=Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50) OX=226186 GN=nfo PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008775 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01261 all species →	AP_endonuc_2	Xylose isomerase-like TIM barrel	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001719 all species →	Family	AP endonuclease 2	Interproscan
IPR018246 all species →	Binding_site	AP endonuclease 2, zinc binding site	Interproscan
IPR013022 all species →	Domain	Xylose isomerase-like, TIM barrel domain	Interproscan
IPR036237 all species →	Homologous_superfamily	Xylose isomerase-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21445 all species →	ENDONUCLEASE IV ENDODEOXYRIBONUCLEASE IV	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003906 all species →	Molecular Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0008081 all species →	Molecular Function	phosphoric diester 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
K10771	APEX1; AP endonuclease 1	EC:3.1.11.2	DNA repair and recombination proteins	ko03400	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_003130-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

18.1Max TPM

5.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.72	7.05
polyp at pH7 6	18	17	3.26	6.99
coral polyp · control treatment	16	16	9.07	18.12
coral polyp · oil and dispersant treatment	16	16	7.27	14.70
coral polyp · oil treatment	16	16	7.99	15.99
coral polyp · dispersant treatment	16	16	3.87	9.73
Polyp	10	9	2.68	6.17

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.05
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.03
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.78
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.66
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.25
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.76
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.25
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.18
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.09
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.73
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.72
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.47
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.17
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.92
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.73
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.99
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.70
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.65
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.50
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.80
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.79
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.73
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.68
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.65
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.40
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.89
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.29
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.06
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.04
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.55
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.81
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.12
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.30
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.79
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.06
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.42
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.23
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.36
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.32
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.39
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.10
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.32
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.51
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.74
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.13
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.94
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.70
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.65
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.79
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.29
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.79
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.07
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.06
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.77
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.60
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.86
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.36
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.81
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.57
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.33
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.56
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.99
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.03
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.99
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.11
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.88
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.70
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.13
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.76
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.56
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.40
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.33
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.71
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.46
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.73
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.56
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.43
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.41
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.79
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.75
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.22
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.84
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.67
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.58
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.09
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.17
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.40
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.33
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.52
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.37
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.37
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.19
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.72
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.