Gene detail

Detailed information of OS493_036831-T1 in Lophelia pertusa

Genomic Location: scaffold_385:248674...258666
NR annotation: KAJ7388603.1, hypothetical protein OS493_036831 [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
Q8IY18	Structural maintenance of chromosomes protein 5 OS=Homo sapiens OX=9606 GN=SMC5 PE=1 SV=2
Q8CG46	Structural maintenance of chromosomes protein 5 OS=Mus musculus OX=10090 GN=Smc5 PE=1 SV=1
Q5ZJY5	Structural maintenance of chromosomes protein 5 OS=Gallus gallus OX=9031 GN=SMC5 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003514 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13476 all species →	AAA_23	AAA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR027131 all species →	Family	Structural maintenance of chromosomes protein 5	Interproscan
IPR038729 all species →	Domain	Rad50/SbcC-type AAA domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45916 all species →	STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0030915 all species →	Cellular Component	Smc5-Smc6 complex	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	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_036831-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_036831-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

84TPM > 0

7Conditions

39.6Max TPM

3.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	6	0.84	4.38
polyp at pH7 6	18	9	1.39	4.76
coral polyp · control treatment	16	15	6.28	39.65
coral polyp · oil and dispersant treatment	16	15	4.42	29.11
coral polyp · oil treatment	16	16	4.45	8.03
coral polyp · dispersant treatment	16	16	3.90	11.19
Polyp	10	7	1.12	2.69

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.38
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.95
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.53
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.44
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.71
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.13
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
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359510	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
SRR11359520	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
SRR11359522	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
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.76
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.04
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.79
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.56
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.18
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.01
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.61
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.10
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.07
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
SRR11359503	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
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.65
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.65
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.40
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.89
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.12
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.67
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.31
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.84
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.45
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.08
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.89
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.69
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.25
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.01
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.55
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	29.11
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.17
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.10
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.07
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.86
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.24
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.18
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.07
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.46
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.97
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.10
SRR16706005	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	0.94
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.94
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.58
SRR16705945	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	8.03
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.54
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.40
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.20
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.70
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.44
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.31
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.88
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.18
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.70
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.35
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.35
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.59
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.57
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.19
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.29
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.49
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.20
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.27
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.90
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.88
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.19
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.80
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.60
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.57
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.86
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.55
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.21
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.69
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.21
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.92
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.41
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.09
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.08
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.79
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	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.