Gene detail

Detailed information of OS493_028727-T1 in Lophelia pertusa

Genomic Location: scaffold_168:285267...285656
NR annotation: KAJ7326005.1, hypothetical protein OS493_028727, partial [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
Q9WVF7	DNA polymerase epsilon catalytic subunit A OS=Mus musculus OX=10090 GN=Pole PE=1 SV=3
Q07864	DNA polymerase epsilon catalytic subunit A OS=Homo sapiens OX=9606 GN=POLE PE=1 SV=5
Q9VCN1	DNA polymerase epsilon catalytic subunit 1 OS=Drosophila melanogaster OX=7227 GN=PolE1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002978 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_028727-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR042087 all species →	Homologous_superfamily	DNA polymerase family B, thumb domain	Interproscan
IPR029703 all species →	Family	DNA polymerase epsilon catalytic subunit	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10670 all species →	DNA POLYMERASE EPSILON CATALYTIC SUBUNIT A	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000278 all species →	Biological Process	mitotic cell cycle	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0006272 all species →	Biological Process	leading strand elongation	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006287 all species →	Biological Process	base-excision repair, gap-filling	Interproscan
GO:0006297 all species →	Biological Process	nucleotide-excision repair, DNA gap filling	Interproscan
GO:0008310 all species →	Molecular Function	single-stranded DNA 3'-5' DNA exonuclease activity	Interproscan
GO:0008622 all species →	Cellular Component	epsilon DNA polymerase complex	Interproscan
GO:0045004 all species →	Biological Process	DNA replication proofreading	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

No KEGG orthology assignment for OS493_028727-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_028727-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

103TPM > 0

7Conditions

49.5Max TPM

2.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	1.99	4.43
polyp at pH7 6	18	17	1.74	4.29
coral polyp · control treatment	16	16	4.66	49.53
coral polyp · oil and dispersant treatment	16	14	2.48	20.36
coral polyp · oil treatment	16	15	1.92	4.83
coral polyp · dispersant treatment	16	16	2.16	3.64
Polyp	10	8	0.87	2.12

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.43
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.48
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.06
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.82
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.55
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.44
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.41
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.32
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.09
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.04
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.83
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.73
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.28
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.06
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.01
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.67
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.64
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.29
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.80
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.67
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.93
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.73
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.93
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.73
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.24
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.18
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.13
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.11
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.88
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.81
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.54
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.51
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.53
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.18
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.17
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.08
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.96
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.87
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.78
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.75
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.64
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.43
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.80
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.67
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.50
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.23
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.14
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.36
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.29
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.02
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.22
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.95
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.87
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.27
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.15
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.76
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.55
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.45
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.45
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.05
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.83
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.97
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.05
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.01
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.95
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.28
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.71
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.28
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.04
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.97
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.95
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.26
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.64
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.55
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.44
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.30
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.17
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.98
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.87
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.05
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.75
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.56
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.41
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.22
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.89
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.31
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.20
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.12
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.92
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.83
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.58
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.63
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.42
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.15
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.05
SRR7746667	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.