Gene detail

Detailed information of OS493_013005-T1 in Lophelia pertusa

Genomic Location: scaffold_34:2161596...2178983
NR annotation: KAJ7373412.1, DNA polymerase alpha subunit B [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005301 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08418 all species →	Pol_alpha_B_N	DNA polymerase alpha subunit B N-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013627 all species →	Domain	DNA polymerase alpha, subunit B, N-terminal	Interproscan
IPR043034 all species →	Homologous_superfamily	DNA polymerase alpha, subunit B, N-terminal domain superfamily	Interproscan
IPR016722 all species →	Family	DNA polymerase alpha, subunit B	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23061 all species →	DNA POLYMERASE 2 ALPHA 70 KDA SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005658 all species →	Cellular Component	alpha DNA polymerase:primase complex	Interproscan
GO:0006270 all species →	Biological Process	DNA replication initiation	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_013005-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_013005-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

73.7Max TPM

3.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	10	0.75	2.77
polyp at pH7 6	18	11	1.04	3.70
coral polyp · control treatment	16	15	6.02	62.22
coral polyp · oil and dispersant treatment	16	14	6.61	73.70
coral polyp · oil treatment	16	14	2.16	6.20
coral polyp · dispersant treatment	16	15	3.12	6.24
Polyp	10	8	1.99	5.00

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.77
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.82
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.54
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.41
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.33
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.20
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.17
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.79
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.78
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.76
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
SRR11359499	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
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
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.70
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.56
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.34
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.99
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.95
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.38
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.16
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.99
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.90
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.90
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.87
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
SRR11359502	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
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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.19
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.11
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.97
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.48
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.15
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.12
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.99
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.63
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.29
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.05
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.78
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.22
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.70
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.19
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.85
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.98
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.18
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.12
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.94
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.94
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.46
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.04
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.86
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.83
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.74
SRR16705945	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	6.20
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.33
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.05
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.42
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.17
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.02
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.34
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.75
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.48
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.25
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.14
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.99
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.96
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.43
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.24
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.14
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.60
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.85
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.70
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.57
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.24
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.96
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.82
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.25
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.15
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.05
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.27
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.06
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.03
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.94
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.42
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.76
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.77
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.72
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.