Gene detail

Detailed information of OS493_022967-T1 in Lophelia pertusa

Genomic Location: scaffold_99:250806...258791
NR annotation: KAJ7378433.1, DNA-(apurinic or apyrimidinic site) lyase [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
A0MTA1	DNA repair nuclease APEX1 OS=Danio rerio OX=7955 GN=apex1 PE=1 SV=1
P28352	DNA repair nuclease/redox regulator APEX1 OS=Mus musculus OX=10090 GN=Apex1 PE=1 SV=2
P43138	DNA repair nuclease/redox regulator APEX1 OS=Rattus norvegicus OX=10116 GN=Apex1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003223 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03372 all species →	Exo_endo_phos	Endonuclease/Exonuclease/phosphatase family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036691 all species →	Homologous_superfamily	Endonuclease/exonuclease/phosphatase superfamily	Interproscan
IPR020848 all species →	Conserved_site	AP endonuclease 1, conserved site	Interproscan
IPR004808 all species →	Family	AP endonuclease 1	Interproscan
IPR005135 all species →	Domain	Endonuclease/exonuclease/phosphatase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22748 all species →	AP ENDONUCLEASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0004519 all species →	Molecular Function	endonuclease activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0004518 all species →	Molecular Function	nuclease activity	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0003906 all species →	Molecular Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0008081 all species →	Molecular Function	phosphoric diester hydrolase activity	Interproscan
GO:0008311 all species →	Molecular Function	double-stranded DNA 3'-5' DNA exonuclease 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_022967-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

104TPM > 0

7Conditions

14.2Max TPM

3.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	5.74	12.03
polyp at pH7 6	18	17	5.65	14.20
coral polyp · control treatment	16	16	2.19	5.59
coral polyp · oil and dispersant treatment	16	15	1.65	3.67
coral polyp · oil treatment	16	16	2.22	5.93
coral polyp · dispersant treatment	16	16	1.75	4.71
Polyp	10	7	2.67	5.11

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	-	12.03
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.45
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.20
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.94
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.82
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.31
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.12
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.07
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.40
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.06
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.89
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.85
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.75
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.48
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.86
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.47
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.20
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.65
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.78
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.43
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.00
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.64
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.38
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.08
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.99
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.86
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.17
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.83
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.27
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.06
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.73
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.59
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.44
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.50
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.10
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.44
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.35
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.09
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.85
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.49
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.44
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.41
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.25
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.16
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.12
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.11
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.69
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.67
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.21
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.21
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.16
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.13
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.13
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.83
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.60
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.43
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.28
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.14
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.89
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.93
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.34
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.02
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.52
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.36
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.32
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.14
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.48
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.41
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.35
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.34
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.26
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.08
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.77
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.71
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.63
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.52
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.51
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.33
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.61
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.32
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.28
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.14
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.99
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.85
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.81
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.78
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.11
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.70
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.27
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.93
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.23
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.09
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.31
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
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.