Gene detail

Detailed information of OS493_040548-T1 in Lophelia pertusa

Genomic Location: scaffold_2481:54...3725
NR annotation: KAJ7375535.1, DNA polymerase delta subunit 3, 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
Q5ZK28	DNA polymerase delta subunit 3 OS=Gallus gallus OX=9031 GN=POLD3 PE=1 SV=2
Q9EQ28	DNA polymerase delta subunit 3 OS=Mus musculus OX=10090 GN=Pold3 PE=1 SV=2
Q15054	DNA polymerase delta subunit 3 OS=Homo sapiens OX=9606 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
IPR041913 all species →	Homologous_superfamily	DNA polymerase delta subunit 3 superfamily	Interproscan
IPR019038 all species →	Family	DNA polymerase delta subunit 3	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

No KEGG orthology assignment for OS493_040548-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_040548-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

87TPM > 0

7Conditions

106.2Max TPM

4.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	10	1.56	4.72
polyp at pH7 6	18	7	0.97	4.48
coral polyp · control treatment	16	16	6.16	43.07
coral polyp · oil and dispersant treatment	16	16	9.92	106.24
coral polyp · oil treatment	16	16	4.73	10.95
coral polyp · dispersant treatment	16	14	5.03	14.08
Polyp	10	8	2.03	4.67

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.72
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.26
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.98
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.32
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.14
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.64
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.72
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.69
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.34
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.25
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.48
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.60
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.48
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.17
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.63
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.47
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	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
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.07
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.08
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.52
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.24
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.88
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.29
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.06
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.97
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.75
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.63
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.41
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.79
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.57
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.16
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.24
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.96
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.27
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.01
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.36
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.04
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.98
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.97
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.78
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.05
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.66
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.62
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.30
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.83
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.95
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.35
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.13
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.66
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.83
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.27
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.62
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.59
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.92
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.03
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.65
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.28
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.08
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.52
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.98
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.78
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.63
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.43
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.99
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.11
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.78
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.39
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.93
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.30
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.67
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.58
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.90
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.75
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.47
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.19
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.29
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.