Gene detail

Detailed information of OS493_025718-T1 in Lophelia pertusa

Genomic Location: scaffold_128:700638...704378
NR annotation: KAJ7383842.1, DNA polymerase epsilon subunit 4 [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
A6QQ14	DNA polymerase epsilon subunit 4 OS=Bos taurus OX=9913 GN=POLE4 PE=3 SV=1
Q9NR33	DNA polymerase epsilon subunit 4 OS=Homo sapiens OX=9606 GN=POLE4 PE=1 SV=2
Q9CQ36	DNA polymerase epsilon subunit 4 OS=Mus musculus OX=10090 GN=Pole4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002445 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00808 all species →	CBFD_NFYB_HMF	Histone-like transcription factor (CBF/NF-Y) and archaeal histone	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009072 all species →	Homologous_superfamily	Histone-fold	Interproscan
IPR050568 all species →	Family	Transcription and DNA Replication Regulators	Interproscan
IPR003958 all species →	Domain	Transcription factor CBF/NF-Y/archaeal histone domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10252 all species →	HISTONE-LIKE TRANSCRIPTION FACTOR CCAAT-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046982 all species →	Molecular Function	protein heterodimerization activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006261 all species →	Biological Process	DNA-templated DNA replication	Interproscan
GO:0008622 all species →	Cellular Component	epsilon DNA polymerase complex	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
K03506	POLE4; DNA polymerase epsilon subunit 4	EC:2.7.7.7	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_025718-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

110TPM > 0

7Conditions

95.1Max TPM

10.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.87	20.37
polyp at pH7 6	18	18	13.11	37.43
coral polyp · control treatment	16	16	10.35	78.91
coral polyp · oil and dispersant treatment	16	16	9.43	95.05
coral polyp · oil treatment	16	16	5.28	10.44
coral polyp · dispersant treatment	16	16	5.92	15.27
Polyp	10	10	17.75	26.11

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.37
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.97
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.94
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.14
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.96
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.56
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.83
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.84
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.57
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.91
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.87
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.49
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.46
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.12
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.70
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.20
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.16
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.58
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.43
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.67
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.98
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.47
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.21
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.80
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.19
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.94
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.90
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.17
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.02
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.90
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.71
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.33
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.22
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.61
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.91
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.96
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.36
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.93
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.79
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.86
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.79
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.76
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.05
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.52
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.51
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.46
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.32
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.70
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.94
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.67
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.05
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.01
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.90
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.39
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.13
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.81
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.03
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.81
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.30
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.23
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.16
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.88
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.51
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.02
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.95
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.79
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.44
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.13
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.06
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.81
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.83
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.33
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.24
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.38
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.08
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.69
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.92
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.20
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.96
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.87
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.66
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.27
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.37
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.66
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.06
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.64
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.93
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.88
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.79
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.70
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.62
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.15
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.78
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.41
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.04
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.66
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	26.11
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	22.82
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	20.73
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.81
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	19.44
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	17.95
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	15.25
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	11.79
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.53

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.