Gene detail

Detailed information of OS493_015782-T1 in Lophelia pertusa

Genomic Location: scaffold_48:467049...469986
NR annotation: KAJ7333699.1, DNA-directed RNA polymerase I subunit rpa2 [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
A1L2H9	Replication protein A 32 kDa subunit-B OS=Xenopus laevis OX=8355 GN=rpa2-b PE=2 SV=1
Q6IP18	Replication protein A 32 kDa subunit-A OS=Xenopus laevis OX=8355 GN=rpa2-a PE=1 SV=1
Q6DFS2	Replication protein A 32 kDa subunit OS=Xenopus tropicalis OX=8364 GN=rpa2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006404 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08784 all species →	RPA_C	Replication protein A C terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR014892 all species →	Domain	Replication protein A, C-terminal	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR040260 all species →	Family	Replication factor A protein-like	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13989 all species →	REPLICATION PROTEIN A-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0000781 all species →	Cellular Component	chromosome, telomeric region	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005662 all species →	Cellular Component	DNA replication factor A complex	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0035861 all species →	Cellular Component	site of double-strand break	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_015782-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_015782-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

109TPM > 0

7Conditions

90.9Max TPM

16.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	21.95	38.16
polyp at pH7 6	18	18	20.10	38.35
coral polyp · control treatment	16	16	15.78	90.93
coral polyp · oil and dispersant treatment	16	16	12.52	80.09
coral polyp · oil treatment	16	16	14.17	29.12
coral polyp · dispersant treatment	16	16	11.00	26.44
Polyp	10	9	20.95	38.86

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.16
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.14
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.26
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.97
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.82
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.51
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.80
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.61
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.27
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.36
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.19
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.71
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.99
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.73
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.93
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.68
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.35
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.35
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.73
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.15
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.92
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.60
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.55
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.22
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.27
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.48
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.65
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.52
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.88
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.78
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.02
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.18
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.68
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.93
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.97
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.68
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.20
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.56
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.76
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.93
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.78
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.26
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.04
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.93
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.29
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.97
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.27
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.66
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	80.09
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.38
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.98
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.73
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.83
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.60
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.24
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.76
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.05
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.37
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.68
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.41
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.37
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.34
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.64
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.78
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.12
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.07
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.14
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.45
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.82
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.29
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.23
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.10
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.32
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.31
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.48
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.89
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.80
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.30
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.36
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.01
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.44
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.01
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.04
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.58
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.89
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.83
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.70
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.59
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.43
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.24
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.92
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.51
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.93
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.10
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	38.86
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	31.12
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	30.94
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	28.66
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	26.34
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.28
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.63
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	14.27
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.39
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.