Gene detail

Detailed information of OS493_040297-T1 in Lophelia pertusa

Genomic Location: scaffold_2012:2458...4730
NR annotation: KAJ7381581.1, 60S acidic ribosomal protein P1-alpha 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
P35244	Replication protein A 14 kDa subunit OS=Homo sapiens OX=9606 GN=RPA3 PE=1 SV=1
Q9CQ71	Replication protein A 14 kDa subunit OS=Mus musculus OX=10090 GN=Rpa3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009092 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08661 all species →	Rep_fac-A_3	Replication factor A protein 3	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR013970 all species →	Family	Replication factor A protein 3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15114 all species →	REPLICATION PROTEIN A3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	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:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0006298 all species →	Biological Process	mismatch 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_040297-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_040297-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

99TPM > 0

7Conditions

48.9Max TPM

5.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	15	6.44	15.87
polyp at pH7 6	18	15	5.31	11.81
coral polyp · control treatment	16	16	6.96	48.92
coral polyp · oil and dispersant treatment	16	13	5.58	44.28
coral polyp · oil treatment	16	15	4.78	11.43
coral polyp · dispersant treatment	16	16	4.25	10.57
Polyp	10	9	5.80	17.68

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.87
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.34
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.37
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.60
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.87
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.41
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.09
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.06
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.86
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.64
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.56
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.86
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.71
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.41
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.25
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	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
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.81
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.31
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.91
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.81
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.75
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.46
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.51
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.38
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.26
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.84
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.43
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.20
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.43
SRR11359500	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	48.92
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.37
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.81
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.37
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.27
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.01
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.67
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.29
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.87
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.79
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.53
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.21
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.89
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.24
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.19
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.90
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.28
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.53
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.87
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.87
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.01
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.86
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.62
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.23
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.66
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.87
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.74
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.62
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.17
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
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.43
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.34
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.70
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.69
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.53
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.31
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.52
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.51
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.54
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.24
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.22
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.93
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.61
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.60
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.35
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.57
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.06
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.85
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.67
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.11
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.67
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.32
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.15
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.13
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.88
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.16
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.91
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.50
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.82
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.63
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.68
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.87
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.81
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.35
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.69
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.25
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.76
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.