Gene detail

Detailed information of XP_032228199.2 in Nematostella vectensis

Genomic Location: NC_064040.1:5167530...5178718
NR annotation: XP_032228199.2, tRNA pseudouridine synthase Pus10 isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032372308.2

ATACCTCACAGCGGTTTTAGTaattttcaagatggcggacaagCTTGTGTTTCGACGACTGGTAAAAAAATCTTAGGAAATCAAGACATCAGGAAACTTCAGGAATAAGACAATGGAAGCAGACTTATGTAATGCCCCTAAAGTCGAAGAAGACTTCTCCACGAACGTGAAGGCGATAGCAGAATCGCTGTACGAACTGAACTTGTGCGTGCGCTGCATTTTGCGCTTTCTCAAAGAAAAGACGCCGTCTGCGTACGAGGGAAATAATTCATCCATTGCTAAGTATATAGAAGAGGAATATGGACTTGAATACATTCTGAAAGAACAGGATACTGAACACAACAATTATGACACAATCTGTAAAGGGTGTCTAGGAATACTCCAAAATGGATGTGATACCCCTATTGTCAACAAGATAGTAGACACTGTCCAGAGCTCAGGGTATGAGTTTGAGAGCTTCACATTTGCTATCTCTATTCCTCTTTCCACTATGGCCTATCAGCACTCATTACTACttcatttaaaagaaaaattcaGCAAGTTTTATGATGCTGTACGTACAGCTGATGACCTGCCGTCAATCAAAGAGGTCATTAAGTGGGTTTGTGGGCCAGCAGTTGGCAATGCACTTGGTGTTTATTTTAAACATGAGAGTCCatttaaaatttcaatatCATTCCATAGTGAGGGTGCTGAAAAATCTTTAGATTTCCTATCTGAGGTCGATCCATCAAGATTCAcagaaaagaagaagaaaaagCGTGCTCCAGAAGTTCCTCTCTACTCAATATCATCAATAAAGAAAGCTCTGGCAGTGTTGTCCTCTGCTGAAGAAATGAGAAGGTTTACTTCTTGTCCACCTGATGTGCCTGTTGCTCAGTGTGTCTGCCAGCAGATTGTATGTTCTCATGGCTCATTGCTTATTGGAGGCCGCTACAATAAGTATTCAAGATGTCTACCACAGACTCCTTGGTTAATTGACGGGGAACGACTCAAAGAATCGTCAGTGCAGgAAAAGATCATTAATATTATTGGACCCCCAATTCAAGCGGATGATTGTCGATTCTCCTCTTCTGGTCGTGAGGACATTGATGTTAGGATGCTTGGAACAGGTCGTCCATTTGTGTTAGAGTTTGTGAATCCTCATAGAACACTTCTAGACGAGGATTTCCTCTCGGATATGCAAAAGCAAATTAACTCCTCGACTAAAGAAATCGCAGTCAGTGGCCTCCAAGTCATCACAAAaGGGGAATACAGTATTTTAAAAGACGgggagacaaagaaaactaagtGCTACAGTGCACTAATCTGGACGAAAGAGCTGGTTCCGCAGACGGAGCTTGACAAGCTAGCTGATATCAAGGATCTTAGGATTGAACAGAAAACTCCCCTTAGAGTATTACACAGACGGCCTCTTGCAGTTCGTGTGAGGGAGGTTCATACGATGTCTGCCCAACGTATTGATGATCATCACTTCAAACTCTTCCTCAAGACAATGGCTGGGACTTATGTCAAGGAGTTTGTTCATGGGGACTTTGGCCGGACGAAACCGAATTTGGGGACGCTACTCGGAGTGGAATCGGACATACTGGAACTTGACGTGGAGTCGGTAGATGTTGAATGGCCACCCGTACGCAAGTGAACTACGAAGCAAAGTGTTAAGATGTCTATTCCTGCGCAAGTGCACCACGAAGCGAAGAGTTAAGGCGACAACTCAATTTGCTCAAAACAAGCAGTCTGCAGCAGTCTGACAAGCTATTTCCGGACTTTAACgcttactgtcgaatccgttgtatcgcgtattttcaaaacaacgatttgttttttttttcttttggtattttctgttccgccaatcagattcttgccatctctcgcctagtacagcgcctggctttctgtcgcgacactgtctggttttcgtccagaggatgGCCAGGGAAGttcacaaagcgagactctgattggctcagaatggttttactgacggaacagaaaatcaaaacatgcgggtcgcgatacaacggatttaACAGAAAAAAACCCCGAGAAACACAATGCCAAGGCGTTTCACCAAATAGTTTGAAGGAAGAAATGTAGTAAATGATGTCTCGTTCGAAAAATCATAGGCAATACCTTCTTCTTTAAAACTGTCTGATCTGCTTTTACCAGTAAACATCTTTAATAAGTAAACAAGTTTGTTCTTAAACTTTATTACAAAACAACTAGAAAAATACTTCGCTCAGACGTGCTTTACATCGATTCAAAATAAATAGTGAAATTCAAAACA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3MIT2	tRNA pseudouridine synthase Pus10 OS=Homo sapiens OX=9606 GN=PUS10 PE=1 SV=1
Q9D3U0	tRNA pseudouridine synthase Pus10 OS=Mus musculus OX=10090 GN=Pus10 PE=1 SV=1
Q6ING2	tRNA pseudouridine synthase Pus10 OS=Xenopus laevis OX=8355 GN=pus10 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003642 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21238 all species →	Pus10_C	Pus10, C-terminal	Domain	Interproscan
PF21237 all species →	Pus10_N_euk	Eukaryotic Pus10, N-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR048741 all species →	Domain	Pus10-like, C-terminal	Interproscan
IPR039894 all species →	Family	tRNA pseudouridine synthase Pus10-like	Interproscan
IPR020103 all species →	Homologous_superfamily	Pseudouridine synthase, catalytic domain superfamily	Interproscan
IPR048742 all species →	Domain	Pus10, N-terminal, eukaryotes	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21568 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0009982 all species →	Molecular Function	pseudouridine synthase activity	Interproscan
GO:0031119 all species →	Biological Process	tRNA pseudouridine synthesis	Interproscan
GO:0001522 all species →	Biological Process	pseudouridine synthesis	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0009451 all species →	Biological Process	RNA modification	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
K07583	PUS10; tRNA pseudouridine synthase 10	EC:5.4.99.25	Transfer RNA biogenesis	ko03016	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_032228199.2 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

37TPM > 0

16Conditions

13.4Max TPM

4.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	8.91	13.42
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	4.97	5.92
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	3.65	3.73
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	3.95	4.75
whole 6 week old aboral regenerate · regenerate uncut	3	3	4.63	5.03
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	1.87	5.60
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	4.73	7.38
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	7.89	8.55
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	4.61	7.14
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	3.62	5.61
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	5.04	5.90
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	4.98	8.35
whole 6 week old aboral regenerate · regenerate 60hpa	3	2	4.35	6.68
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	4.91	8.19
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	5.36	8.24
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	1.98	5.93

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	13.42
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	7.01
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	6.29
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	5.92
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	5.85
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	3.14
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.73
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.72
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.52
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	4.75
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	3.70
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	3.40
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	5.03
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	4.92
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.93
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	5.60
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	7.38
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	6.82
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	8.55
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	7.97
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	7.15
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	7.14
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	6.70
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	5.61
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	5.25
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	5.90
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	4.68
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	4.53
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	8.35
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	6.60
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	6.68
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	6.38
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	0.00
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	8.19
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	6.53
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	8.24
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	7.85
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	5.93
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.