Gene detail

Detailed information of OS493_019627-T1 in Lophelia pertusa

Genomic Location: scaffold_69:1282965...1300343
NR annotation: KAJ7378931.1, Nucleoporin-like protein 2 [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
Q5ZI22	Nucleoporin NUP42 OS=Gallus gallus OX=9031 GN=NUP42 PE=2 SV=1
O15504	Nucleoporin NUP42 OS=Homo sapiens OX=9606 GN=NUP42 PE=1 SV=1
Q5RB98	Nucleoporin NUP42 OS=Pongo abelii OX=9601 GN=NUP42 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006618 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13634 all species →	Nucleoporin_FG	Nucleoporin FG repeat region	Family	Interproscan
PF18044 all species →	zf-CCCH_4	CCCH-type zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036855 all species →	Homologous_superfamily	Zinc finger, CCCH-type superfamily	Interproscan
IPR000571 all species →	Domain	Zinc finger, CCCH-type	Interproscan
IPR051767 all species →	Family	Nucleoporin NUP42 domain-containing protein	Interproscan
IPR025574 all species →	Repeat	Nucleoporin FG repeat	Interproscan
IPR041367 all species →	Domain	E3 ligase, CCCH-type zinc finger	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46527 all species →	NUCLEOPORIN-LIKE PROTEIN 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046872 all species →	Molecular Function	metal ion 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14321	NUPL2, NUP42, CG1; nucleoporin-like protein 2	-	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_019627-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

35.5Max TPM

7.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.78	15.01
polyp at pH7 6	18	18	8.63	11.04
coral polyp · control treatment	16	16	9.38	22.25
coral polyp · oil and dispersant treatment	16	16	7.43	35.48
coral polyp · oil treatment	16	16	7.50	11.36
coral polyp · dispersant treatment	16	16	6.02	13.42
Polyp	10	9	6.47	14.80

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	-	15.01
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.69
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.09
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.17
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.58
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.21
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.56
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.11
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.99
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.88
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.70
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.58
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.48
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.30
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.82
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.50
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.94
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.47
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.04
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.84
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.24
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.23
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.07
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.93
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.26
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.96
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.87
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.71
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.99
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.95
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.52
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.48
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.21
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.45
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.25
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.42
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.48
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.75
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.82
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.51
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.42
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.66
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.36
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.34
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.66
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.33
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.66
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.54
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.57
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.48
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.87
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.73
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.73
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.08
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.01
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.77
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.63
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.40
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.28
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.19
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.09
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.31
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.23
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.59
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.43
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.36
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.45
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.27
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.26
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.13
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.69
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.57
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.22
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.74
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.33
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.11
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.94
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.91
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.99
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.42
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.29
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.26
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.21
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.69
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.61
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.12
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.07
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.07
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.89
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.12
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.33
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.31
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.11
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.69
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.21
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.80
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	10.89
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.71
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.10
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.62
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.31
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.50
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.71
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.