Gene detail

Detailed information of OS493_033439-T1 in Lophelia pertusa

Genomic Location: scaffold_265:224577...231811
NR annotation: KAJ7389117.1, regulation of microtubule polymerization or depolymerization [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
Q0P426	SKA complex subunit 2 OS=Danio rerio OX=7955 GN=ska2 PE=2 SV=2
B5X5N3	SKA complex subunit 2 OS=Salmo salar OX=8030 GN=ska2 PE=2 SV=1
Q4R8E8	SKA complex subunit 2 OS=Macaca fascicularis OX=9541 GN=SKA2 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009610 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11362 all species →	DUF3161	Protein of unknown function (DUF3161)	Family	Interproscan
PF16740 all species →	SKA2	Spindle and kinetochore-associated protein 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR042091 all species →	Domain	Ska2, N-terminal	Interproscan
IPR026762 all species →	Family	Spindle and kinetochore-associated protein 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32017 all species →	SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000278 all species →	Biological Process	mitotic cell cycle	Interproscan
GO:0000940 all species →	Cellular Component	outer kinetochore	Interproscan
GO:0005876 all species →	Cellular Component	spindle microtubule	Interproscan
GO:0007059 all species →	Biological Process	chromosome segregation	Interproscan
GO:0008017 all species →	Molecular Function	microtubule binding	Interproscan
GO:0051301 all species →	Biological Process	cell division	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
K26095	SKA2; spindle and kinetochore-associated protein 2	-	Chromosome and associated proteins	ko03036	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_033439-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

52.5Max TPM

8.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.35	15.46
polyp at pH7 6	18	18	8.34	15.64
coral polyp · control treatment	16	16	8.39	52.54
coral polyp · oil and dispersant treatment	16	16	7.00	44.85
coral polyp · oil treatment	16	16	8.23	21.77
coral polyp · dispersant treatment	16	16	4.88	11.35
Polyp	10	9	11.30	27.55

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	-	15.46
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.40
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.78
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.92
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.45
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.16
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.67
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.84
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.81
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.39
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.39
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.36
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.62
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.23
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.19
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.36
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.63
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.64
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.81
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.78
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.64
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.51
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.41
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.34
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.78
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.72
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.64
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.29
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.75
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.95
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.93
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.19
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.64
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.54
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.91
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.31
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.04
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.38
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.20
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.13
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.98
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.03
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.96
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.34
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.12
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.46
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.47
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.39
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.85
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.75
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.14
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.10
SRR16705976	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	6.91
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.65
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.22
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.90
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.60
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.53
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.42
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.88
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.78
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.12
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.77
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.98
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.59
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.58
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.75
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.55
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.30
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.01
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.99
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.67
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.48
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.03
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.57
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.09
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.61
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.66
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.35
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.21
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.55
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.05
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.04
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.95
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.05
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.93
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.77
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.68
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.21
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.95
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.32
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.56
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.05
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	27.55
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	23.92
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.08
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	14.81
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.28
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.86
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.20
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.03
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.25
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.