Gene detail

Detailed information of OS493_008780-T1 in Lophelia pertusa

Genomic Location: scaffold_20:3966330...3978614
NR annotation: KAJ7386629.1, Nuclear pore complex subunit [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
Q9BTX1	Nucleoporin NDC1 OS=Homo sapiens OX=9606 GN=NDC1 PE=1 SV=2
Q5RBY5	Nucleoporin NDC1 OS=Pongo abelii OX=9601 GN=NDC1 PE=2 SV=1
Q7SZC5	Nucleoporin NDC1 OS=Danio rerio OX=7955 GN=ndc1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004883 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09531 all species →	Ndc1_Nup	Nucleoporin protein Ndc1-Nup	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019049 all species →	Family	Nucleoporin protein Ndc1-Nup	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13269 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006999 all species →	Biological Process	nuclear pore organization	Interproscan
GO:0030674 all species →	Molecular Function	protein-macromolecule adaptor activity	Interproscan
GO:0070762 all species →	Cellular Component	nuclear pore transmembrane ring	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
K14315	NDC1, TMEM48; nucleoporin NDC1	-	Messenger RNA biogenesis	ko03019	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_008780-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

110TPM > 0

7Conditions

19.5Max TPM

6.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.05	8.88
polyp at pH7 6	18	18	7.28	9.81
coral polyp · control treatment	16	16	7.76	18.54
coral polyp · oil and dispersant treatment	16	16	5.71	19.55
coral polyp · oil treatment	16	16	7.04	10.38
coral polyp · dispersant treatment	16	16	5.16	9.52
Polyp	10	10	7.21	11.22

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.88
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.46
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.35
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.35
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.11
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.43
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.39
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.23
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.65
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.58
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.25
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.84
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.73
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.71
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.94
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.81
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.68
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.61
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.38
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.29
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.24
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.72
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.63
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.06
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.05
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.99
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.83
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.50
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.32
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.24
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.55
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.12
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.02
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.54
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.07
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.89
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.12
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.77
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.03
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.85
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.66
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.23
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.19
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.69
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.54
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.31
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.36
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.12
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.55
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.21
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.04
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.99
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.68
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.33
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.84
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.77
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.44
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.32
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.13
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.64
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.09
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.58
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.52
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.38
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.85
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.35
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.62
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.56
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.28
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.07
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.69
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.55
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.31
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.26
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.32
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.11
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.77
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.52
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.90
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.56
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.56
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.20
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.99
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.93
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.42
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.07
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.04
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.85
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.62
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.45
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.56
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.22
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.04
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.99
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.63
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.89
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.43
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.53
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.46
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.97

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.