Gene detail

Detailed information of OS493_003999-T1 in Lophelia pertusa

Genomic Location: scaffold_8:1206057...1209265
NR annotation: KAJ7387036.1, hypothetical protein OS493_003999 [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
Q640Z6	Nuclear pore complex protein Nup153 OS=Xenopus laevis OX=8355 GN=nup153 PE=1 SV=1
H2QII6	E3 SUMO-protein ligase RanBP2 OS=Pan troglodytes OX=9598 GN=RANBP2 PE=1 SV=1
P49792	E3 SUMO-protein ligase RanBP2 OS=Homo sapiens OX=9606 GN=RANBP2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004961 (this species only)
Ubiquitin family	UBD\|ZnF\|NZF · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00641 all species →	zf-RanBP	Zn-finger in Ran binding protein and others	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR026054 all species →	Family	Nuclear pore complex protein	Interproscan
IPR036443 all species →	Homologous_superfamily	Zinc finger, RanBP2-type superfamily	Interproscan
IPR001876 all species →	Domain	Zinc finger, RanBP2-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23193 all species →	NUCLEAR PORE COMPLEX PROTEIN NUP	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005643 all species →	Cellular Component	nuclear pore	Interproscan
GO:0006405 all species →	Biological Process	RNA export from nucleus	Interproscan
GO:0006606 all species →	Biological Process	protein import into nucleus	Interproscan
GO:0008139 all species →	Molecular Function	nuclear localization sequence binding	Interproscan
GO:0017056 all species →	Molecular Function	structural constituent of 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_003999-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_003999-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

55.4Max TPM

16.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.47	23.77
polyp at pH7 6	18	18	14.03	21.90
coral polyp · control treatment	16	16	21.84	55.43
coral polyp · oil and dispersant treatment	16	16	23.08	44.69
coral polyp · oil treatment	16	16	16.15	27.06
coral polyp · dispersant treatment	16	16	16.25	30.90
Polyp	10	9	5.37	8.96

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.77
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.66
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.45
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.93
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.28
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.55
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.84
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.55
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.28
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.58
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.10
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.90
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.87
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.98
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.78
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.81
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.57
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.90
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.12
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.68
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.61
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.27
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.10
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.07
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.69
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.54
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.88
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.99
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.49
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.75
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.57
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.21
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.90
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.43
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.77
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.80
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.76
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.71
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.87
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.32
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.96
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.13
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.89
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.71
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.06
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.34
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.74
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.69
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.06
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.35
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.52
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.51
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.16
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.14
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.95
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.73
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.32
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.95
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.94
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.60
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.06
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.49
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.38
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.11
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.90
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.15
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.75
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.70
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.74
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.02
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.96
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.41
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.87
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.34
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.33
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.14
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.90
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.51
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.70
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.64
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.20
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.84
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.05
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.60
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.08
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.01
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.45
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.17
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.34
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.73
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.96
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.51
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.58
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.21
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.26
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.55
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.87
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.21
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.