Gene detail

Detailed information of OS493_036823-T1 in Lophelia pertusa

Genomic Location: scaffold_385:208212...210550
NR annotation: KAJ7388595.1, Structural maintenance of chromosomes protein 5 [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
Q805A1	Structural maintenance of chromosomes protein 5 OS=Xenopus laevis OX=8355 GN=smc5 PE=2 SV=1
Q8IY18	Structural maintenance of chromosomes protein 5 OS=Homo sapiens OX=9606 GN=SMC5 PE=1 SV=2
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

No Pfam domain signature was detected for OS493_036823-T1. This gene does have a gene model — the search simply returned no hit.

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

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

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_036823-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_036823-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

109TPM > 0

7Conditions

121.3Max TPM

15.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	13.11	24.40
polyp at pH7 6	18	18	11.03	17.21
coral polyp · control treatment	16	16	22.79	121.34
coral polyp · oil and dispersant treatment	16	16	16.49	101.42
coral polyp · oil treatment	16	16	17.82	31.36
coral polyp · dispersant treatment	16	16	14.85	33.13
Polyp	10	9	13.78	31.44

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.40
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.60
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.54
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.61
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.76
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.38
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.33
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.05
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.17
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.97
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.74
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.63
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.14
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.47
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.12
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.79
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.73
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.48
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.21
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.18
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.07
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.84
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.09
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.73
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.66
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.62
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.22
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.16
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.78
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.79
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.62
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.12
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.59
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.46
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.06
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	121.34
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.24
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.07
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.17
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.05
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.95
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.86
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.24
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.68
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.04
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.88
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.08
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.93
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.28
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.18
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.42
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.03
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.66
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.99
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.82
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.93
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.29
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.30
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.54
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.50
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.26
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.77
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.87
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.23
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.76
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.36
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.01
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.75
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.53
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.60
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.34
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.46
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.75
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.08
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.66
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.50
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.34
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.17
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.61
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.13
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.50
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.52
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.59
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.34
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.85
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.64
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.10
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.91
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.67
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.21
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.85
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.98
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.43
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.96
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	31.44
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	22.55
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	21.77
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	17.23
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.31
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	14.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.88
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.80
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.84
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.