Gene detail

Detailed information of OS493_023348-T1 in Lophelia pertusa

Genomic Location: scaffold_103:263537...273522
NR annotation: KAJ7390637.1, DNA polymerase delta subunit 3 [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
Q5ZK28	DNA polymerase delta subunit 3 OS=Gallus gallus OX=9031 GN=POLD3 PE=1 SV=2
Q15054	DNA polymerase delta subunit 3 OS=Homo sapiens OX=9606 GN=POLD3 PE=1 SV=2
Q9EQ28	DNA polymerase delta subunit 3 OS=Mus musculus OX=10090 GN=Pold3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004772 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09507 all species →	CDC27	DNA polymerase subunit Cdc27	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019038 all species →	Family	DNA polymerase delta subunit 3	Interproscan
IPR041913 all species →	Homologous_superfamily	DNA polymerase delta subunit 3 superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR17598 all species →	DNA POLYMERASE DELTA SUBUNIT 3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0043625 all species →	Cellular Component	delta DNA polymerase complex	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0006271 all species →	Biological Process	DNA strand elongation involved in DNA replication	Interproscan
GO:0006297 all species →	Biological Process	nucleotide-excision repair, DNA gap filling	Interproscan
GO:1904161 all species →	Biological Process	DNA synthesis involved in UV-damage excision 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
K03504	POLD3; DNA polymerase delta subunit 3	-	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_023348-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

30.8Max TPM

4.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.05	7.23
polyp at pH7 6	18	16	4.87	10.65
coral polyp · control treatment	16	16	5.28	30.84
coral polyp · oil and dispersant treatment	16	16	4.49	28.66
coral polyp · oil treatment	16	16	4.46	7.45
coral polyp · dispersant treatment	16	16	4.34	9.85
Polyp	10	9	3.90	7.86

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.23
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.54
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.32
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.27
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.77
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.50
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.20
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.15
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.09
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.94
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.73
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.46
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.40
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.55
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.44
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.65
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.66
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.24
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.12
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.96
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.74
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.87
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.86
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.68
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.48
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.22
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.16
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.01
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.59
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.09
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.67
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.14
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.73
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.70
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.69
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.55
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.03
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.52
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.13
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.93
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.85
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.77
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.34
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.66
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.16
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.52
SRR16705993	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	3.51
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.38
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.87
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.76
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.75
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.69
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.09
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.57
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.14
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.45
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.76
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.58
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.66
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.67
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.58
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.57
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.53
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.21
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.90
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.66
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.62
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.37
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.30
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.25
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.20
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.85
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.94
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.53
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.37
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.15
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.79
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.70
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.92
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.70
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.55
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.48
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.07
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.18
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.61
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.12
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.22
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.19
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.17
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.19
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.24
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.01
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.02
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.