Gene detail

Detailed information of OS493_028557-T1 in Lophelia pertusa

Genomic Location: scaffold_166:46641...51647
NR annotation: KAJ7370946.1, Nuclear pore complex protein Nup50 [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
Q9UKX7	Nuclear pore complex protein Nup50 OS=Homo sapiens OX=9606 GN=NUP50 PE=1 SV=2
O08587	Nuclear pore complex protein Nup50 OS=Rattus norvegicus OX=10116 GN=Nup50 PE=2 SV=2
Q9JIH2	Nuclear pore complex protein Nup50 OS=Mus musculus OX=10090 GN=Nup50 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006882 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08911 all species →	NUP50	NUP50 (Nucleoporin 50 kDa)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011993 all species →	Homologous_superfamily	PH-like domain superfamily	Interproscan
IPR045255 all species →	Family	Ran binding protein RanBP1-like	Interproscan
IPR015007 all species →	Domain	Nuclear pore complex, NUP2/50/61	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23138 all species →	RAN BINDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006606 all species →	Biological Process	protein import into nucleus	Interproscan
GO:0005643 all species →	Cellular Component	nuclear pore	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_028557-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_028557-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

11.9Max TPM

4.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.65	6.25
polyp at pH7 6	18	18	5.72	7.95
coral polyp · control treatment	16	16	4.68	11.94
coral polyp · oil and dispersant treatment	16	16	5.27	9.05
coral polyp · oil treatment	16	16	4.23	7.79
coral polyp · dispersant treatment	16	16	3.31	6.00
Polyp	10	9	2.56	3.88

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.25
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.16
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.77
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.67
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.63
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.59
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.52
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.32
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.47
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.16
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.10
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.98
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.87
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.74
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.66
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.62
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.12
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.09
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.95
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.55
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.16
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.99
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.36
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.35
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.91
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.78
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.66
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.35
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.11
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.97
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.82
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.53
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.33
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.17
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.74
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.94
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.06
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.20
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.14
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.06
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.58
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.57
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.22
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.17
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.21
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.84
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.10
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.84
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.58
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.12
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.05
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.87
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.37
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.15
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.54
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.09
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.68
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.51
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.38
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.26
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.62
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.19
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.12
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.84
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.81
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.79
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.10
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.73
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.27
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.26
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.87
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.53
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.02
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.96
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.94
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.34
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.73
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.50
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.82
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.59
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.97
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.74
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.57
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.96
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.51
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.04
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.70
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.44
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.10
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.91
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.55
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.28
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.27
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.88
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.82
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.21
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.85
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.55
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.39
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.17
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.35
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.