Gene detail

Detailed information of OS493_019789-T1 in Lophelia pertusa

Genomic Location: scaffold_70:1057208...1070207
NR annotation: KAJ7372344.1, Non-structural maintenance of chromosomes element 4 A [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
Q2TBI1	Non-structural maintenance of chromosomes element 4 homolog A OS=Bos taurus OX=9913 GN=NSMCE4A PE=2 SV=1
Q9NXX6	Non-structural maintenance of chromosomes element 4 homolog A OS=Homo sapiens OX=9606 GN=NSMCE4A PE=1 SV=2
A6QPC8	EP300-interacting inhibitor of differentiation 3 OS=Bos taurus OX=9913 GN=EID3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005991 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF15412 all species →	Nse4-Nse3_bdg	Binding domain of Nse4/EID3 to Nse3-MAGE	Domain	Interproscan
PF08743 all species →	Nse4_C	Nse4 C-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029225 all species →	Domain	Nse4/EID protein, Nse3/MAGE-binding domain	Interproscan
IPR014854 all species →	Domain	Non-structural maintenance of chromosome element 4, C-terminal	Interproscan
IPR027786 all species →	Family	Nse4/EID family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16140 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K22825	NSMCE4, NSE4; non-structural maintenance of chromosomes element 4	-	DNA repair and recombination proteins	ko03400	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_019789-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

102TPM > 0

7Conditions

36.9Max TPM

2.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	2.37	4.56
polyp at pH7 6	18	15	1.81	3.31
coral polyp · control treatment	16	16	3.87	31.27
coral polyp · oil and dispersant treatment	16	16	3.56	36.87
coral polyp · oil treatment	16	15	1.86	4.18
coral polyp · dispersant treatment	16	16	2.21	4.91
Polyp	10	7	1.41	4.50

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.56
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.66
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.41
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.39
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.25
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.12
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.82
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.75
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.69
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.65
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.11
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.97
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.87
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.62
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.11
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.01
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.73
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.31
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.79
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.74
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.68
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.67
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.61
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.60
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.47
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.92
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.84
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.73
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.71
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.65
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.12
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.74
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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.27
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.60
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.77
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.46
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.35
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.05
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.90
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.89
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.80
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.52
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.44
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.33
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.81
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.72
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.61
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.41
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.89
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.49
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.08
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.75
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.22
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.06
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.95
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.77
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.48
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.43
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.32
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.18
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.79
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.69
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.64
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.54
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.33
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.16
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.05
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.99
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.80
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.42
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.02
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.83
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.67
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.91
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.81
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.59
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.75
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.43
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.14
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.72
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.57
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.25
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.04
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.49
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.36
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.50
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.74
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.68
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.41
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.92
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.85
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.