Gene detail

Detailed information of OS493_000050-T1 in Lophelia pertusa

Genomic Location: scaffold_1:521278...525968
NR annotation: KAJ7394248.1, recQ-mediated genome instability protein 1 [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
A4IF98	RecQ-mediated genome instability protein 1 OS=Bos taurus OX=9913 GN=RMI1 PE=2 SV=1
Q9D4G9	RecQ-mediated genome instability protein 1 OS=Mus musculus OX=10090 GN=Rmi1 PE=2 SV=1
Q9H9A7	RecQ-mediated genome instability protein 1 OS=Homo sapiens OX=9606 GN=RMI1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004229 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16099 all species →	RMI1_C	Recq-mediated genome instability protein 1, C-terminal OB-fold	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR032199 all species →	Domain	RecQ-mediated genome instability protein 1, C-terminal OB-fold domain	Interproscan

PANTHER

No PANTHER signature was recorded for OS493_000050-T1 in Lophelia pertusa.

Gene Ontology

GO term	Category	Description	Source
GO:0000166 all species →	Molecular Function	nucleotide binding	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_000050-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_000050-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

104TPM > 0

7Conditions

44.4Max TPM

5.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	8.06	14.49
polyp at pH7 6	18	17	7.68	12.80
coral polyp · control treatment	16	15	5.24	44.36
coral polyp · oil and dispersant treatment	16	14	3.15	30.05
coral polyp · oil treatment	16	16	2.74	8.28
coral polyp · dispersant treatment	16	16	1.90	3.70
Polyp	10	9	9.57	20.70

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	-	14.49
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.78
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.49
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.89
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.67
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.04
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.67
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.36
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.32
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.00
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.19
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.04
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.39
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.34
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.82
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.95
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.80
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.69
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.29
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.04
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.69
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.77
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.68
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.10
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.10
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.04
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.47
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.43
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.38
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.21
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.12
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.36
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.76
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.16
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.44
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.22
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.83
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.01
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.99
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.54
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.79
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.61
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.30
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.25
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.35
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.29
SRR16705990	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	30.05
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.26
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.69
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.50
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.13
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.11
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.80
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.78
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.70
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.52
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.19
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	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	8.28
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.31
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.38
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.67
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.24
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.19
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.69
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.07
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.03
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.90
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.18
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.01
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.98
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.71
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.64
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.35
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.03
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.95
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.90
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.38
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.96
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.84
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.68
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.63
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.33
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.82
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.77
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.42
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	20.70
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	18.22
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	16.70
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	16.65
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.97
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.49
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.30
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.26
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.