Gene detail

Detailed information of OS493_001798-T1 in Lophelia pertusa

Genomic Location: scaffold_4:1232523...1235778
NR annotation: KAJ7375066.1, Poly(A)+ RNA export protein rae1 [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
Q7ZWF0	mRNA export factor OS=Danio rerio OX=7955 GN=rae1 PE=2 SV=2
Q5FVA9	mRNA export factor OS=Xenopus tropicalis OX=8364 GN=rae1 PE=2 SV=1
Q9W2E7	Protein Rae1 OS=Drosophila melanogaster OX=7227 GN=Rae1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002173 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10971 all species →	MRNA EXPORT FACTOR AND BUB3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000972 all species →	Biological Process	transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005643 all species →	Cellular Component	nuclear pore	Interproscan
GO:0006405 all species →	Biological Process	RNA export from nucleus	Interproscan
GO:0043130 all species →	Molecular Function	ubiquitin 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
K13341	PEX7, PTS2R; peroxin-7	-	Peroxisome	ko04146	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_001798-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

107TPM > 0

7Conditions

26.3Max TPM

7.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	6.21	9.37
polyp at pH7 6	18	17	7.08	12.75
coral polyp · control treatment	16	16	9.59	26.32
coral polyp · oil and dispersant treatment	16	16	6.32	11.75
coral polyp · oil treatment	16	16	8.13	18.05
coral polyp · dispersant treatment	16	16	6.72	12.12
Polyp	10	9	4.58	6.82

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.37
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.28
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.61
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.50
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.38
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.22
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.06
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.74
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.64
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.36
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.36
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.25
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.21
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.45
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.69
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.35
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.24
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.75
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.43
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.32
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.19
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.45
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.91
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.02
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.60
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.44
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.44
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.40
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.19
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.17
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.77
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.27
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.87
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.32
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.57
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.81
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.21
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.10
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.53
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.58
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.48
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.31
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.08
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.98
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.87
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.83
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.01
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.79
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.75
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.91
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.59
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.17
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.78
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.33
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.29
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.93
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.74
SRR16705977	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	4.43
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.31
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.20
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.57
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.28
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.05
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.51
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.18
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.68
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.41
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.41
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.20
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.81
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.76
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.95
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.83
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.92
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.77
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.15
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.12
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.27
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.12
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.82
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.65
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.81
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.54
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.01
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.89
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.81
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.65
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.60
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.16
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.15
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.07
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.84
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.06
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.36
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.82
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.76
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.57
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.23
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.58
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.90
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.69
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.34
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.91
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.