Gene detail

Detailed information of OS493_013581-T1 in Lophelia pertusa

Genomic Location: scaffold_37:1686573...1690631
NR annotation: KAJ7392207.1, Condensin-2 complex subunit D3 [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
Q6GN08	Condensin-2 complex subunit D3-L OS=Xenopus laevis OX=8355 GN=ncapd3.L PE=1 SV=1
Q6ZQK0	Condensin-2 complex subunit D3 OS=Mus musculus OX=10090 GN=Ncapd3 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001997 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12765 all species →	Cohesin_HEAT	HEAT repeat associated with sister chromatid cohesion	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR026003 all species →	Repeat	HEAT repeat associated with sister chromatid cohesion protein	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR026971 all species →	Family	Condensin subunit 1/Condensin-2 complex subunit D3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14222 all species →	CONDENSIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000779 all species →	Cellular Component	condensed chromosome, centromeric region	Interproscan
GO:0000799 all species →	Cellular Component	condensin complex	Interproscan
GO:0007076 all species →	Biological Process	mitotic chromosome condensation	Interproscan
GO:0010032 all species →	Biological Process	meiotic chromosome condensation	Interproscan
GO:0042393 all species →	Molecular Function	histone binding	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_013581-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_013581-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

79TPM > 0

7Conditions

15.7Max TPM

1.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	13	1.39	2.83
polyp at pH7 6	18	8	1.05	4.51
coral polyp · control treatment	16	14	2.27	15.72
coral polyp · oil and dispersant treatment	16	10	1.65	6.39
coral polyp · oil treatment	16	13	1.53	3.80
coral polyp · dispersant treatment	16	15	1.92	4.21
Polyp	10	6	0.98	2.90

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.83
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.40
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.29
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.96
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.95
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.89
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.87
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.78
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.71
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.67
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.26
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	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
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.51
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.49
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.29
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.38
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.75
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.04
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.92
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
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	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
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	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
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.72
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.95
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.68
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.42
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.35
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.19
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.85
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.51
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.82
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.81
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.54
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.42
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.36
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.39
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.66
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.51
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.29
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.98
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.37
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.40
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.80
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.53
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.45
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.35
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.28
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.13
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.89
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.27
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.17
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.04
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.93
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.90
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.70
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.21
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.11
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.81
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.16
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.96
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.27
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.17
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.76
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.72
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.70
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.97
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.77
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.65
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.36
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.17
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.90
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.01
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.71
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.28
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.99
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.92
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
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.