Gene detail

Detailed information of XP_032242372.2 in Nematostella vectensis

Genomic Location: NC_064037.1:11184109...11195471
NR annotation: XP_032242372.2, S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 isoform X2 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC5516601

ATGGCGGACGAACGAAAAGCTCGACCCTTCCCGTTCATAACATGGATTTGTCTCACTTTATTTGGTCTTTTGATTATTTTTGTTGCTGTGTTCGAAGAGCATAGCGAGGGCAAGCCAGCGGCCGCAGCGCTCCGCACAGTGTACAGTTACTGGATGCAAGTGAGGAAGTCAGCATATACCTTACTTTTTGGAGGGGCTGTTTTGGTTTATATTTATGGCCTTGCTATGGGGGAGCGCCGAGAAGCTACTGCTGCACCTGAGGCCACACCCAGTCAAACAAAACAGGAAGTAAAAGAGATAAAAAGTAAAGTTTCAGCTACCCTGAGGATTTTTTATGCCACGCAGACTGGTACAGCCAAGAAATTCTCTGAAGAGCTAATGAAAATATCAATGCAACAAGGAATGGATTGCAGCTGTGAGAATTTGCAAGGTTATGAAGCAGAGGATAATCTAGCCAATGAGAAATCTACCTGTGTGTTCATTGTGCCAACATACACTGACGGCAAGCCTCCAAGGGGTGCAGAGTGGTTTTACAGCTGGCTAGAGGACTCAACCAATGACTGCCGTGTGTCAAAGTCACTACTTAGTCAAATTAACTATGCTGTGTTTGGCTTAGGAAATTCTTCTTACGAGGGTCAGTTTAACTTGGTTGCCAAAAATATTGACAAATGGCTTTCATCTTTGAGTGCGAAGAGGGTGATGCCTGTAACACTTGGAGATGAGAACACAGTTAACAGCAGACATGGAGGTCTTGAAGCCGATTTTCAAGTGTGGTGCAAAACATTTTTTTCACTTGTTAAATCACACACATTATGTGAGTGTGGAAAACAAGAAACCTGTCAGGAAACAAGCAAGTCTCAGGAAGAAACATCTCAAGCATGTGACTACGAGAGTACAAGTGATGGAGATTCTGAGGATGAGGATACAGCTGATGGCCTTGTTGATATGGAAGATCTTGGTCCTGCCGTCCAAAAAATTAAAAAAGCAAAGAAGCAAAGGGAGATAGAGGAGGATTCTCATAAAAACACAGTTGCTAAAGAGATGGTTACACCAGTGATTCGACAGTCACTTACCAAGCAAGGTTACAAGATAATAGGATCACATTCGGGAGTGAAGATTTGTAGGTGGACCAAGTCAATGCTACGTGGCCGGGGAGGCTGTTATAAGCACACATTCTATGGTATAGAAAGCCATCGCTGTATGGAAACCACCCCAAGTCTTGCATGTGCCAATAAGTGTGTTTTCTGTTGGAGACATCACACTAACCCTGTGGGCACAGAATGGCGTTGGCAGATGGATGATCCTCAGATGATTGTTGAAGGCGCAATGCAGAACCACTACAACATGATAAAACAGTTCCGAGGTGTCCCTGGTGTCAAGCCTGAGAGGTTTGAAGAGGGCATGAAGATTAAGCACTGTGCTCTATCACTCGTTGGGGAGCCTATTATGTACCCAAAAATTAATGAGCTCATCAAGCTCCTGCATGGACATGGCATCTCTTCATTTCTTGTCACAAATGCACAGTTTCCGGATGCTATAAAGGACCTCCTACCAGTGACGCAGCTTTATGTCAGTGTTGACGCAGGCACCAAAGAAAGCCTGAAAAAGATTGACCGCCCACTCTTTAGGGATTTCTGGCCTCGGTTTCTCGACAGCCTTAAAGCCCTAGCAGATAAGGGTCAAAGGACTGTCTACCGCTTAACACTTGTCAAGTCATGGAATGTTGAAGAGATACAGTCATATGTAGAGCTTGTGTCTCTTGGAAAACCTGACTTCATAGAGGTTAAAGGTGTGACATACTGTGGCGAGTCCAAGGCATCGACACTGACAATGGCTAATATCCCTTGGCACCAGGAGGTTGTAGGGTTTGTACGGAAGCTTGAAGACCAGCTACCAGATTATGAACTAGCCTCTGAGCATGAGCATTCCAACTGTGTGCTTCTTGCTCACAAGAAGTTCAAGGTCAATGGTGAATGGCATACATGGATTGATTATACCAAATTCCATCAGCTGATAGAAAAATATGAGGAGAGCAATGGCGAGGAGACCTTCACATCCGCTGACTACATGGAAAGGAACCCTGAATGGTCTGTTTTTGGGCACTCACAGCGAGGCTTTGATCCTGAGGAGACTCGGTGGTACCGCAAGAACCGAAAAGATATCAGTGGATGCTGA

Transcript

rna-XM_032386481.2

AGTACCCGGCAGGACTTTAGAACCGCAGGcgtcaagatggcggacgaacGAAAAGCTCGACCCTTCCCGTTCATAACATGGATTTGTCTCACTTTATTTggtcttttgattatttttgttgctgtgTTCGAAGAGCATAGCGAGGGCAAGCCAGCGGCCGCAGCGCTCCGCACAGTGTACAGTTACTGGATGCAAGTGAGGAAGTCAGCATATACCTTACTTTTTGGAGGGGCTGTTTTGGTTTATATTTATGGCCTTGCTATGGGGGAGCGCCGAGAAGCTACTGCTGCACCTGAGGCCACACCCAGTCAAACAAAACAGGAAGTAAAAGAGATAAAAAGTAAAGTTTCAGCTACCCtgaggattttttatgccacGCAGACTGGTACAGCCAAGAAATTCTCTGAAGAGCTAATGAAAATATCAATGCAACAAGGAATGGATTGCAGCTGTGAGAATTTGCAAGGTTATGAAGCAGAGGATAATCTAGCCAATGAGaaATCTACCTGTGTGTTCATTGTGCCAACATACACTGACGGCAAGCCTCCAAGGGGTGCAGAGTGGTTTTACAGCTGGCTAGAGGACTCAACCAATGACTGCCGTGTGTCAAAGTCACTACTTAGTCAAATTAACTATGCTGTGTTTGGCTTAGGAAATTCTTCTTACGAGGGTCAGTTTAACTTGGTTGCCAAAAATATTGACAAATGGCTTTCATCTTTGAGTGCGAAGAGGGTGATGCCTGTAACACTTGGAGATGAGAACACAGTTAACAGCAGACATGGAGGTCTTGAAGCCGATTTTCAAGTGTGgtgcaaaacatttttttcacttgtTAAATCACACACATTATGTGAGTGTGGAAAACAAGAAACCTGTCAGGAAACAAGCAAGTCTCAGGAAGAAACATCTCAAGCATGTGACTACGAGAGTACAAGTGATGGAGATTCTGAGGATGAGGATACAGCTGATGGCCTTGTTGATATGGAAGATCTTGGTCCTGCCGtccaaaaaattaaaaaagcaaaGAAGCAAAGGGAGATAGAGGAGGATTCTCATAAAAACACAGTTGCTAAAGAGATGGTTACACCAGTGATTCGACAGTCACTTACCAAGCAAGGTTACAAGATAATAGGATCACATTCGGGAGTGAAGATTTGTAGGTGGACCAAGTCAATGCTACGTGGCCGGGGAGGCTGTTATAAGCACACATTCTATGGTATAGAAAGCCATCGCTGTATGGAAACCACCCCAAGTCTTGCATGTGCCAATAAGTGTGTTTTCTGTTGGAGACATCACACTAACCCTGTGGGCACAGAATGGCGTTGGCAGATGGATGATCCTCAGATGATTGTTGAAGGCGCAATGCAGAACCACTACAACATGATAAAACAGTTCCGAGGTGTCCCTGGTGTCAAGCCTGAGAGGTTTGAAGAGGGCATGAAGATTAAGCACTGTGCTCTATCACTCGTTGGGGAGCCTATTATGTACCCAAAAATTAATGAGCTCATCAAGCTCCTGCATGGACATGGCATCTCTTCATTTCTTGTCACAAATGCACAGTTTCCGGATGCTATAAAGGACCTCCTACCAGTGACGCAGCTTTATGTCAGTGTTGACGCAGGCACCAAAGAAAGCCTGAAAAAGATTGACCGCCCACTCTTTAGGGATTTCTGGCCTCGGTTTCTCGACAGCCTTAAAGCCCTAGCAGATAAGGGTCAAAGGACTGTCTACCGCTTAACACTTGTCAAGTCATGGAATGTTGAAGAGATACAGTCATATGTAGAGCTTGTGTCTCTTGGAAAACCTGACTTCATAGAGGTTAAAGGTGTGACATACTGTGGCGAGTCCAAGGCATCGACACTGACAATGGCTAATATCCCTTGGCACCAGGAGGTTGTAGGGTTTGTACGGAAGCTTGAAGACCAGCTACCAGATTATGAACTAGCCTCTGAGCATGAGCATTCCAACTGTGTGCTTCTTGCTCACAAGAAGTTCAAGGTCAATGGTGAATGGCATACATGGATTGATTATACCAAATTCCATCAGCTGATAGAAAAATATGAGGAGAGCAATGGCGAGGAGACCTTCACATCCGCTGACTACATGGAAAGGAACCCTGAATGGTCTGTTTTTGGGCACTCACAGCGAGGCTTTGATCCTGAGGAGACTCGGTGGTACCGCAAGAACCGAAAAGATATCAGTGGATGCTGATGTGATTGACTTCTCAGGGAATCAGAGGCAGTTACATGCCTGGGAGGGGAGCCACCTACACACATCCTTGActtatttcttattgaaggatcatcctttttccatatgatatctatCACTGCACAGCTGCCCTTACACTCTCTCTTccataaagaaaaagaaaaaggataaGAGCAGTTAACCTTACAGTACTTTTATCTTAAGAATGGTCAGCATTACACTTTTGTACAAAATCAAAGTCAAACTTTAGACCATTCATTTTGCTCTTCCATAGCAATTACTGGAGGGTGAGATATGTGGCTACTGATCACAAAACATGGACAAATGTTTCTgttcaaatattttcaatgacTTGTGAATGCATGTTGCTGCTCCAGCTAGGCTATTTATATTTGGTTGAGGGTGTACCatgttttttaaaacataGAGATAGCTGTTGTTACAATATTTCAATTGTGCTTCCTCGCTCTGGATGGtttaaagagaaaaaacgcTAATAAAATACTCAATAATGGTG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q2KHP8	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 OS=Xenopus laevis OX=8355 GN=tyw1 PE=2 SV=1
Q9NV66	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 OS=Homo sapiens OX=9606 GN=TYW1 PE=1 SV=2
Q5REF9	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 OS=Pongo abelii OX=9601 GN=TYW1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004277 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00258 all species →	Flavodoxin_1	Flavodoxin	Domain	Interproscan
PF08608 all species →	Wyosine_form	Wyosine base formation	Family	Interproscan
PF04055 all species →	Radical_SAM	Radical SAM superfamily	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007197 all species →	Domain	Radical SAM	Interproscan
IPR013785 all species →	Homologous_superfamily	Aldolase-type TIM barrel	Interproscan
IPR034556 all species →	Family	S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase	Interproscan
IPR008254 all species →	Domain	Flavodoxin/nitric oxide synthase	Interproscan
IPR029039 all species →	Homologous_superfamily	Flavoprotein-like superfamily	Interproscan
IPR013917 all species →	Domain	tRNA wybutosine-synthesis	Interproscan
IPR001094 all species →	Domain	Flavodoxin-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13930 all species →	S-ADENOSYL-L-METHIONINE-DEPENDENT TRNA 4-DEMETHYLWYOSINE SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0051536 all species →	Molecular Function	iron-sulfur cluster binding	Interproscan
GO:0008033 all species →	Biological Process	tRNA processing	Interproscan
GO:0051539 all species →	Molecular Function	4 iron, 4 sulfur cluster binding	Interproscan
GO:0010181 all species →	Molecular Function	FMN binding	Interproscan
GO:0031591 all species →	Biological Process	wybutosine biosynthetic process	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
K15449	TYW1; tRNA wybutosine-synthesizing protein 1	EC:4.1.3.44	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_032242372.2 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

40TPM > 0

16Conditions

14.9Max TPM

6.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	8.35	10.00
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	6.94	7.91
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	5.87	6.54
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	6.08	6.95
whole 6 week old aboral regenerate · regenerate uncut	3	3	6.12	6.66
whole 6 week old aboral regenerate · regenerate 4hpa	3	2	3.20	6.34
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	5.35	9.05
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	9.00	10.20
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	5.95	9.97
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	5.08	8.12
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	6.85	7.42
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	11.70	14.89
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	11.34	13.27
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	7.30	11.72
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	5.06	7.75
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	2.12	6.36

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	10.00
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	9.16
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	5.89
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	7.91
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	7.28
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	5.63
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	6.54
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	5.63
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	5.45
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	6.95
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	6.30
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	4.98
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	6.66
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	6.08
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	5.62
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	6.34
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	3.25
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	9.05
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	7.01
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	10.20
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	9.25
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	7.55
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	9.97
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	7.88
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	8.12
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	7.13
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	7.42
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	7.11
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	6.02
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	14.89
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	11.17
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	9.05
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	13.27
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	11.11
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	9.65
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	11.72
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	10.18
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	7.75
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	7.42
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	6.36
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.