Gene detail

Detailed information of XP_048588656.1 in Nematostella vectensis

Genomic Location: NC_064042.1:1279082...1287611
NR annotation: XP_048588656.1, regulator of nonsense transcripts 3B isoform X2 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_048732699.1

tgaaAGTCGAGACGAGAGCTGGACCTCATACAAAACGACAACAagttccaagatggcggaagcTGGATAAAAACACCGCTCAACAAAATGGGGAAAACGGAGACAGAGAAAGGAAAATCGcccatcaaaacaaaaagagacaAAGCATTTTTTCAGACCAAGgTGGTGATACGAAGACTGCCTCCTTCACTTAAAGAAGAAGAGCTGAAAGAGTATCTCGGAGATTTGCCTGAGCATGATTTCTTTTACTTTGTGGATGGACAAATGAGTTTTGGGCCTGTACTTTTTTCTCGTGCTTACATCAATTTCAAGAACCAAGAGGACATTATCAAGTTCAGAGACCAGTTTGATGGATCATCTTTTTTTGATAACAAAGGTAATGAGTACCCAGCTGTTGTCGAGTATGCACCGTACCAGGGAGTACCCAGGAAGAAGAACAGGAAAGACGCCAAGTGTGGTACCATAGATGAAGATAAGGACTACCAGTCGTTCCTGCAGTCCTTGGAGGAGGAAACTGAGCCCCTACCAAGTGTAGAGTCACACTTAGAAGAGATTGAGGCTCGCAAGGAAGATAATTCCAAAAAGAGCACGCCCCTCCTGGAGTTCCTAAAAATGAAGAGAAGCATGAGGGCAACATCACGACAGAGTCAGGGGCGTGGAGGATTTGACAAAAGAAAGAGAATAGAAAAATCAGAAGAATCTTCTAAGGGAGTAAAGAAAGGAGGATCAGGCAATAAGGACTCAAAGACCCCACCCAGAGaggagaaaaataaagaagtGAAAAGGTCTGAGGGCAGTCAGGAACAGAGGAAAGATGAGGACAAGAAACTGACCAAGGACTCAAAGGGGCGCCCGGAATCCGCTCGGTCTGGAGGCAGAGGAGACGATAGACGCTCGGGAGGTCGTCGTGAACGTCGGGAGATTGCGAACAGCGACAGTCGTGGTCCTCGCGACAACAAAAATCGGCGAGACGAGGAGCCAAGAAGAGACAGTCGACCGAACAGTCGTAAGGAGCGAGGACCCTATCGCGGCGCCGACAATGCTACGAAAAGCCGAGACGAGTCCGATAACAAAAACGAAACCAAAGCCGACACCGAATCTGCCACAGGTTCTGCGCCGAGGACGACCCGAAAAGAACCCGACGCCAAGGAAGAACGGCGCGAGGTCATTCGGGATAGAGGAGACGGAAGACAGTCCAGAGTCAGAAATAAGGATCGCCCAGACAGGGAAATTTATCAGCCAGGACGTGCACGGACTCGACCCACGGAGACAAACGAAAAAGATGTTAAACCGAGTGGCGAAAAGAGAGACGACGGAGAATCAAAACGGGACCGTGATAGAGACAAGAATCGTGACAAAAATCGTGACAGAAACCGAGAGCGTGAAAAGAACCGCGAGCGTGACAGACGGGATCGTGACAGGGACCGTGGAAAAGAGCGTGAGAGAAACCGTGACAAGGATCGGTATCGTGGTAAACCACGTGACGTGACGTCAGGCGACGCGAAGCCAAAGCCAGAAGAGACTGGTAAAGCTAAAGTCGAGGGTACAGGTGCTACACGGGAAGAAGAGGCTTAGTGTGATGTACGGGAGCAAAAAGATCCTGGATCTGGATTGGGTGATGCTTTGATTCTAgttgaattttgaaatatcATTTTGGATTTTTATGTTTGCCGCACAAATTGTTTTTAGAGTCAAGGAAATTTAATATTTGTCTAACCCCCATAAAGCTCACGTCTCCTAGGCTCCCTGTCTGCCCCATCATCTACTTCCGGTTGTGATCCATCGTTCAGAAACGTGGCTACTTGTTACCTATTATGGTGCGAACGCCAAAGTCTCAGCCTTGTCTCCATGCGGAATCATCATAACACCTGTGACATGTTACTGTCACTCTGCTTTGATTAATTAAAAGGACAACTATTTATCGTTAACCAACCATGTTACAGCGCAATGCTACTGTGGCCTTCTTGGCAGTTTTCTTCACCAGCCAGTCAGCATGGCAAAAAATGCTTGAGTGCATCGAAAGACAATGGAAAGTTTGTGTCAATAAAAAGTTAATGCATGCTAATTGGCTAACtttcttttaacttttttgcTAGCCTTGGTTGCGTGCATCACACTATGAAATTATAACGTACGAGTAGAATCCAGCTTAATAGTTAAAGATAGTTATTGTGCAATTAGCAGTTGACATTCACAAGACAAAAGAGAAGaaatttatgtattttttaattttgctaGTTGCATAGTTGCATGAGTTATAGCATTCTAATATGGTGTATCAACTGGTCAAAATGTAGACAAGCTAAAATGAACAGATATATAGGTACCTCCTGCCATGTCTCATTAATTGgtaaccccccccctcccaaagaaatcctggatccaccccAAGCCTCTTGTATGTAAGTAATCAAACCTGGTAATCCATCAAAGATTTAGTAGTTTACTTAGACTTACAAAATTCAAATGTTTCTGACAGAATGCATTTGGTGCATAATAATGGTTGTGTTGAGTGTTATTCTTGTGTTTTAACTATTGTACAGCTATCAGTCTTCAACAAGATGAACTTGATAGCTTAGATCATTAACTAAACGCATGGTAATAGTTGTACTATtaacatatacatatattagagtggttttccaAATCCTGTGAAatactttttagtttatttagtactaatacaatgtaatgtctttgttatcttttgtTCTTGCGTGACTATTGCACtgtaacaattacattttgtttcacTGGATTTTAAAAACCACTCTACAACTATCATAATTGTTATACTAGTATATAGATGTAATAGTAgtgtttaatgtttttttcctaagACATCTTGAAATAACATATTTctaaaatgtaaaatataaaaaagaatacCTAATATCTCTTTTATGAATTCAATGTAAAAACTACCACTATCAAAGTGATATTTACTCTAAATCTTCTATTAAATCATCAGCTGTTTTTAA

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)	OG0005524 (this species only) · gene tree & orthology

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
IPR005120 all species →	Domain	UPF3 domain	Interproscan
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

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 XP_048588656.1 across 48 RNA-seq samples of Nematostella vectensis. 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.

48Samples

40TPM > 0

16Conditions

14.0Max TPM

7.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	8.67	9.98
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	7.83	11.20
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	6.59	7.78
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	7.98	8.73
whole 6 week old aboral regenerate · regenerate uncut	3	3	7.31	8.52
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	2.88	8.64
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	7.57	12.88
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	10.07	13.96
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	6.12	10.55
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	8.27	8.66
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	7.65	8.71
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	11.01	13.94
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	9.32	10.70
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	7.01	11.22
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	7.51	11.67
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	3.21	9.63

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	9.98
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	8.12
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	7.91
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	11.20
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	6.31
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	5.98
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	7.78
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	6.34
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	5.65
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	8.73
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	7.67
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	7.55
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	8.52
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	7.64
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	5.78
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	8.64
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	12.88
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	9.82
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	13.96
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	8.90
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	7.36
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	10.55
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	7.82
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	8.66
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	8.63
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	7.52
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	8.71
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	7.55
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	6.69
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	13.94
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	10.41
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	8.68
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	10.70
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	9.11
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	8.15
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	11.22
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	9.83
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	11.67
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	10.87
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	9.63
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00

Source: CnidoSite RNA-seq expression matrices (NVECT_TPM, StringTie quantification over 48 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.