Gene detail

Detailed information of OS493_010507-T1 in Lophelia pertusa

Genomic Location: scaffold_25:2556499...2564722
NR annotation: KAJ7392847.1, Regulator of nonsense transcripts 3B [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
Q9BZI7	Regulator of nonsense transcripts 3B OS=Homo sapiens OX=9606 GN=UPF3B PE=1 SV=1
F1QNX7	Regulator of nonsense transcripts 3B OS=Danio rerio OX=7955 GN=upf3b PE=2 SV=1
B0S733	Regulator of nonsense transcripts 3A OS=Danio rerio OX=7955 GN=upf3a PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005592 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03467 all species →	Smg4_UPF3	Smg-4/UPF3 family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR039722 all species →	Family	Nonsense-mediated mRNA decay protein 3	Interproscan
IPR005120 all species →	Domain	UPF3 domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13112 all species →	UPF3 REGULATOR OF NONSENSE TRANSCRIPTS-LIKE PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0045727 all species →	Biological Process	positive regulation of translation	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
K14328	UPF3, RENT3; regulator of nonsense transcripts 3	-	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_010507-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

58.3Max TPM

22.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	20.33	26.94
polyp at pH7 6	18	18	22.42	35.98
coral polyp · control treatment	16	16	26.81	44.74
coral polyp · oil and dispersant treatment	16	16	17.66	38.62
coral polyp · oil treatment	16	16	27.10	45.85
coral polyp · dispersant treatment	16	16	13.90	26.97
Polyp	10	10	34.16	58.33

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.94
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.08
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.46
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.63
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.70
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.50
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.92
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.77
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.21
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.73
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.03
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.77
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.20
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.90
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.79
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.16
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.46
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.98
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.98
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.63
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.08
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.28
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.91
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.97
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.96
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.67
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.42
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.37
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.50
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.15
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.83
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.57
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.17
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.77
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.60
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.27
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.72
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.25
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.32
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.82
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.70
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.46
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.81
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.76
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.29
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.92
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.58
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.33
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.62
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.92
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.08
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.94
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.57
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.20
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.40
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.32
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.18
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.01
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.74
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.37
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.01
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.01
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.75
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.41
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.85
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.22
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.59
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.32
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.28
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.12
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.80
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.24
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.04
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.51
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.06
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.85
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.38
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.46
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.97
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.13
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.58
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.96
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.31
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.96
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.24
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.00
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.69
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.27
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.30
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.18
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.45
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.09
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.52
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	58.33
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	41.29
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	39.15
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	37.16
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	35.94
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	32.65
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	28.78
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	25.51
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	21.77
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	21.07

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.