Gene detail

Detailed information of OS493_004590-T1 in Lophelia pertusa

Genomic Location: scaffold_9:2234280...2246773
NR annotation: KAJ7380996.1, Nucleoporin nup35 [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
Q6P6X9	Nucleoporin NUP35 OS=Danio rerio OX=7955 GN=nup35 PE=1 SV=1
Q8NFH5	Nucleoporin NUP35 OS=Homo sapiens OX=9606 GN=NUP35 PE=1 SV=1
Q8R4R6	Nucleoporin NUP35 OS=Mus musculus OX=10090 GN=Nup35 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002332 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05172 all species →	Nup35_RRM	Nup53/35/40-type RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007846 all species →	Domain	RNA-recognition motif (RRM) Nup35-type domain	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR017389 all species →	Family	Nucleoporin, NUP53	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21527 all species →	NUCLEOPORIN NUP35	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005543 all species →	Molecular Function	phospholipid binding	Interproscan
GO:0006607 all species →	Biological Process	NLS-bearing protein import into nucleus	Interproscan
GO:0006913 all species →	Biological Process	nucleocytoplasmic transport	Interproscan
GO:0006999 all species →	Biological Process	nuclear pore organization	Interproscan
GO:0017056 all species →	Molecular Function	structural constituent of nuclear pore	Interproscan
GO:0031965 all species →	Cellular Component	nuclear membrane	Interproscan
GO:0044613 all species →	Cellular Component	nuclear pore central transport channel	Interproscan
GO:0044615 all species →	Cellular Component	nuclear pore nuclear basket	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
K14313	NUP35, NUP53; nuclear pore complex protein Nup53	-	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_004590-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

33.6Max TPM

13.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.54	22.75
polyp at pH7 6	18	18	11.85	17.42
coral polyp · control treatment	16	16	14.75	25.29
coral polyp · oil and dispersant treatment	16	16	17.44	30.40
coral polyp · oil treatment	16	16	14.81	33.58
coral polyp · dispersant treatment	16	16	10.09	17.31
Polyp	10	10	18.05	31.72

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.75
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.94
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.85
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.85
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.62
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.41
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.78
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.16
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.66
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.51
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.40
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.91
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.69
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.54
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.22
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.97
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.43
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.01
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.42
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.26
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.71
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.70
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.63
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.19
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.68
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.67
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.13
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.74
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.69
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.34
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.99
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.65
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.02
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.39
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.12
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.91
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.29
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.87
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.65
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.57
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.22
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.19
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.19
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.21
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.38
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.38
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.01
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.91
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.27
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.65
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.36
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.80
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.40
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.44
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.08
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.04
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.57
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.56
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.32
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.18
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.52
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.68
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.59
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.93
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.17
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.18
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.09
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.58
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.87
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.61
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.39
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.28
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.37
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.02
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.04
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.90
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.55
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.55
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.04
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.83
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.34
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.31
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.39
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.94
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.92
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.90
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.88
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.12
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.98
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.44
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.75
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.48
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.38
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.20
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.68
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.37
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	31.72
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	23.59
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	22.42
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	21.57
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	18.24
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	17.64
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.98
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.92
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.64
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.82

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.