Gene detail

Detailed information of OS493_005869-T1 in Lophelia pertusa

Genomic Location: scaffold_12:1875624...1877186
NR annotation: KAJ7339471.1, 5' exonuclease Apollo [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
B0V2S2	5' exonuclease Apollo OS=Danio rerio OX=7955 GN=dclre1b PE=2 SV=1
Q9H816	5' exonuclease Apollo OS=Homo sapiens OX=9606 GN=DCLRE1B PE=1 SV=1
D2H8V8	5' exonuclease Apollo OS=Ailuropoda melanoleuca OX=9646 GN=DCLRE1B PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002307 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07522 all species →	DRMBL	DNA repair metallo-beta-lactamase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011084 all species →	Domain	DNA repair metallo-beta-lactamase	Interproscan
IPR036866 all species →	Homologous_superfamily	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23240 all species →	DNA CROSS-LINK REPAIR PROTEIN PSO2/SNM1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000723 all species →	Biological Process	telomere maintenance	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0035312 all species →	Molecular Function	5'-3' DNA exonuclease activity	Interproscan
GO:0036297 all species →	Biological Process	interstrand cross-link repair	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
K15341	DCLRE1B, SNM1B; DNA cross-link repair 1B protein	EC:3.1.-.-	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_005869-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

107TPM > 0

7Conditions

17.6Max TPM

1.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	1.59	2.47
polyp at pH7 6	18	18	1.19	2.88
coral polyp · control treatment	16	16	1.82	17.62
coral polyp · oil and dispersant treatment	16	15	1.60	15.73
coral polyp · oil treatment	16	16	0.89	2.41
coral polyp · dispersant treatment	16	15	0.49	1.67
Polyp	10	9	0.69	2.28

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.47
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.25
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.24
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.06
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.02
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.01
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.94
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.82
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.77
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.57
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.51
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.27
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.01
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.74
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.72
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.59
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.88
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.45
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.86
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.38
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.38
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.30
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.15
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.11
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.08
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.97
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.88
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.74
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.65
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.46
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.36
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.29
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.62
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.79
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.47
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.19
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.08
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.04
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.89
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.74
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.70
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.34
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.30
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.29
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.25
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.24
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.73
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.31
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.24
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.85
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.54
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.53
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.49
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.45
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.42
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.41
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.40
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.41
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.56
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.39
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.23
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.20
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.15
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.63
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.61
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.61
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.52
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.52
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.48
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.36
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.32
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.14
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.67
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.94
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.74
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.48
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.47
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.47
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.44
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.39
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.25
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.23
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.20
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.07
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.06
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.28
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.32
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.06
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.94
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.64
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.34
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.21
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.05
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.04
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.