Gene detail

Detailed information of OS493_036820-T1 in Lophelia pertusa

Genomic Location: scaffold_385:190884...195709
NR annotation: KAJ7388592.1, hypothetical protein OS493_036820 [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
Q802R9	Structural maintenance of chromosomes protein 5 OS=Takifugu rubripes OX=31033 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
IPR038729 all species →	Domain	Rad50/SbcC-type AAA domain	Interproscan
IPR027131 all species →	Family	Structural maintenance of chromosomes protein 5	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
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:0030915 all species →	Cellular Component	Smc5-Smc6 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_036820-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_036820-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

94TPM > 0

7Conditions

26.5Max TPM

2.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	14	1.62	3.31
polyp at pH7 6	18	13	1.75	4.93
coral polyp · control treatment	16	16	4.05	26.49
coral polyp · oil and dispersant treatment	16	14	3.28	21.34
coral polyp · oil treatment	16	15	2.98	6.09
coral polyp · dispersant treatment	16	15	2.46	7.10
Polyp	10	7	0.86	1.83

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.31
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.26
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.95
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.75
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.62
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.24
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.08
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.82
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.74
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.61
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.06
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.06
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.99
SRR11359494	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
SRR11359508	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
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.93
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.68
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.53
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.05
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.61
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.04
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.92
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.89
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.63
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.51
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.49
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.22
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
SRR11359512	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	26.49
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.10
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.31
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.14
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.76
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.66
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.34
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.55
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.35
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.33
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.25
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.14
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.90
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.75
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.53
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.27
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.34
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.42
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.22
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.23
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.14
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.98
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.89
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.88
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.64
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.37
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.28
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.21
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.01
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.96
SRR16705945	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
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.09
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.76
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.40
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.36
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.08
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.88
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.57
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.47
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.19
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.61
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.40
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.01
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.10
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.30
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.07
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.47
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.97
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.86
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.76
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.42
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.11
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.29
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.83
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.77
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.39
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.24
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.06
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.85
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
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.