Gene detail

Detailed information of OS493_000049-T1 in Lophelia pertusa

Genomic Location: scaffold_1:515328...521110
NR annotation: KAJ7394247.1, 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
Q5ZHV8	RecQ-mediated genome instability protein 1 OS=Gallus gallus OX=9031 GN=RMI1 PE=2 SV=1
Q9H9A7	RecQ-mediated genome instability protein 1 OS=Homo sapiens OX=9606 GN=RMI1 PE=1 SV=3
Q9D4G9	RecQ-mediated genome instability protein 1 OS=Mus musculus OX=10090 GN=Rmi1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004252 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21000 all species →	RMI1_N_N	RMI1, N-terminal helical domain	Domain	Interproscan
PF08585 all species →	RMI1_N_C	RMI1, N-terminal OB-fold domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR044881 all species →	Homologous_superfamily	RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily	Interproscan
IPR049363 all species →	Domain	RMI1, N-terminal domain	Interproscan
IPR042470 all species →	Homologous_superfamily	RecQ mediated genome instability protein, N-terminal OB-fold domain superfamily	Interproscan
IPR013894 all species →	Domain	RecQ mediated genome instability protein 1, OB-fold domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14790 all species →	RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1 RMI1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000712 all species →	Biological Process	resolution of meiotic recombination intermediates	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0016604 all species →	Cellular Component	nuclear body	Interproscan
GO:0031422 all species →	Cellular Component	RecQ family helicase-topoisomerase III complex	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_000049-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_000049-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

108TPM > 0

7Conditions

38.8Max TPM

3.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.71	6.08
polyp at pH7 6	18	18	3.92	6.14
coral polyp · control treatment	16	16	3.95	38.77
coral polyp · oil and dispersant treatment	16	16	2.94	33.57
coral polyp · oil treatment	16	16	1.78	4.47
coral polyp · dispersant treatment	16	16	1.39	3.51
Polyp	10	8	3.53	8.92

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.08
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.40
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.69
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.65
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.02
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.60
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.42
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.41
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.28
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.15
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.08
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.90
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.73
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.56
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.40
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.73
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.53
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.78
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.21
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.12
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.83
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.80
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.68
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.53
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.33
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.29
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.15
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.74
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.68
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.53
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.88
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.77
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.39
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.71
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.51
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.30
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.27
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.02
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.94
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.84
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.15
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.12
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.92
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.76
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.67
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.37
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.57
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.80
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.67
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.59
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.48
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.28
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.05
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.99
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.81
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.80
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.53
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.21
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.16
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.07
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.47
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.73
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.35
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.75
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.52
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.46
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.44
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.34
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.25
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.23
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.93
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.67
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.53
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.22
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.51
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.46
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.09
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.02
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.83
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.82
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.60
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.09
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.85
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.84
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.82
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.76
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.44
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.92
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.17
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.69
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.97
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.27
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.11
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.23
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.