Gene detail

Detailed information of OS493_009831-T1 in Lophelia pertusa

Genomic Location: scaffold_23:3095954...3101188
NR annotation: KAJ7363669.1, kinetochore-associated Ndc80 complex subunit ndc80 [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
Q9D0F1	Kinetochore protein NDC80 homolog OS=Mus musculus OX=10090 GN=Ndc80 PE=1 SV=1
O14777	Kinetochore protein NDC80 homolog OS=Homo sapiens OX=9606 GN=NDC80 PE=1 SV=1
Q4R630	Kinetochore protein NDC80 homolog OS=Macaca fascicularis OX=9541 GN=NDC80 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003110 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03801 all species →	Ndc80_HEC	HEC/Ndc80p family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005550 all species →	Family	Kinetochore protein Ndc80	Interproscan
IPR038273 all species →	Homologous_superfamily	Ndc80 domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10643 all species →	KINETOCHORE PROTEIN NDC80	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0031262 all species →	Cellular Component	Ndc80 complex	Interproscan
GO:0051315 all species →	Biological Process	attachment of mitotic spindle microtubules to kinetochore	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_009831-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_009831-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

105TPM > 0

7Conditions

32.6Max TPM

3.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	3.61	5.76
polyp at pH7 6	18	14	2.18	4.88
coral polyp · control treatment	16	16	4.28	32.58
coral polyp · oil and dispersant treatment	16	15	2.90	18.77
coral polyp · oil treatment	16	16	2.53	5.47
coral polyp · dispersant treatment	16	16	1.99	3.88
Polyp	10	10	3.60	16.65

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	-	5.76
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.74
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.53
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.36
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.97
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.68
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.59
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.76
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.56
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.36
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.12
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.04
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.15
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.13
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.91
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.86
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.73
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.71
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.88
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.59
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.46
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.03
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.74
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.72
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.65
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.51
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.03
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.98
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.53
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.77
SRR11359500	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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.58
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.60
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.23
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.45
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.35
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.33
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.39
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.13
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.05
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.63
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.62
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.86
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.78
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.28
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.77
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.09
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.29
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.15
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.11
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.04
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.98
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.97
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.91
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.71
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.61
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.36
SRR16705994	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	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.47
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.65
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.22
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.15
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.12
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.10
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.05
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.03
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.93
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.21
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.74
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.52
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.34
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.97
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.82
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.88
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.57
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.53
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.61
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.59
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.20
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.88
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.77
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.49
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.27
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.17
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.05
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.73
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.52
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	16.65
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.71
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.49
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.83
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.43
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.93
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.92
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.88
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.52

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.