Detailed information of XP_032218455.2 in Nematostella vectensis

Genomic Location: NC_064046.1:6458821...6468716
NR annotation: XP_032218455.2, deubiquitinase OTUD6B isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q8N6M0Deubiquitinase OTUD6B OS=Homo sapiens OX=9606 GN=OTUD6B PE=1 SV=1
Q8K2H2Deubiquitinase OTUD6B OS=Mus musculus OX=10090 GN=Otud6b PE=1 SV=1
Q7ZV00Deubiquitinase OTUD6B OS=Danio rerio OX=7955 GN=otud6b PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006370 (this species only) · gene tree & orthology
Ubiquitin familyDUB|OTU|OTU · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02338
all species →		OTUOTU-like cysteine proteaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR038765
all species →		Homologous_superfamilyPapain-like cysteine peptidase superfamilyInterproscan
IPR050704
all species →		FamilyOTU domain-containing ubiquitin thioesteraseInterproscan
IPR049772
all species →		DomainOTU domain-containing protein 6A/6B, ovarian tumor domainInterproscan
IPR003323
all species →		DomainOTU domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12419
all species →		OTU DOMAIN CONTAINING PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004843
all species →		Molecular Functioncysteine-type deubiquitinase activityInterproscan
GO:0016579
all species →		Biological Processprotein deubiquitinationInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K18342OTUD6; OTU domain-containing protein 6EC:3.4.19.12
Ubiquitin systemko04121deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of XP_032218455.2 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
8.7Max TPM
4.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole 6 week old aboral regenerate · regenerate 96hpa 3 3 5.84 6.54
whole 6 week old aboral regenerate · regenerate 144hpa 3 3 4.91 5.81
whole 6 week old aboral regenerate · regenerate 0hpa 3 3 3.60 3.92
whole 6 week old aboral regenerate · regenerate 2hpa 3 3 3.66 3.99
whole 6 week old aboral regenerate · regenerate uncut 3 3 4.41 5.20
whole 6 week old aboral regenerate · regenerate 4hpa 3 1 1.23 3.68
whole 6 week old aboral regenerate · regenerate 120hpa 3 2 3.97 6.67
whole 6 week old aboral regenerate · regenerate 36hpa 3 3 7.13 8.70
whole 6 week old aboral regenerate · regenerate 24hpa 3 2 3.58 6.07
whole 6 week old aboral regenerate · regenerate 20hpa 3 2 3.09 5.14
whole 6 week old aboral regenerate · regenerate 16hpa 3 3 4.05 4.83
whole 6 week old aboral regenerate · regenerate 72hpa 3 2 4.43 7.31
whole 6 week old aboral regenerate · regenerate 60hpa 3 3 6.62 8.16
whole 6 week old aboral regenerate · regenerate 48hpa 3 1 2.18 6.55
whole 6 week old aboral regenerate · regenerate 8hpa 3 2 3.67 6.22
whole 6 week old aboral regenerate · regenerate 12hpa 3 1 1.61 4.82

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR6320836 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 6.54
SRR6320837 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 6.21
SRR6320863 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 4.76
SRR6320847 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 5.81
SRR6320838 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 4.60
SRR6320841 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 4.33
SRR6320839 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 3.92
SRR6320846 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 3.63
SRR6320840 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 3.27
SRR6320861 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 3.99
SRR6320842 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 3.64
SRR6320848 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 3.37
SRR6320844 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 5.20
SRR6320843 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 4.52
SRR6320845 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 3.51
SRR6320872 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 3.68
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 6.67
SRR6320883 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 5.26
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 8.70
SRR6320851 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 6.92
SRR6320852 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 5.77
SRR6320854 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 6.07
SRR6320853 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 4.69
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 5.14
SRR6320860 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 4.13
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 4.83
SRR6320881 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 3.74
SRR6320858 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 3.57
SRR6320862 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 7.31
SRR6320865 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 5.98
SRR6320864 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 0.00
SRR6320869 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 8.16
SRR6320867 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 6.27
SRR6320866 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 5.44
SRR6320870 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 6.55
SRR6320868 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 0.00
SRR6320871 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 6.22
SRR6320875 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 4.79
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 4.82
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.

Co-expression network

Genes whose expression across the transcriptome samples of Nematostella vectensis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

DirectionPartnersMost correlated partnerPCC
Positively correlated48XP_001640019.20.95274308783947
Negatively correlated4XP_001629182.1-0.670533562675044

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Nematostella vectensis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

DatasetTissue / stageCellsCell typesThis geneMarker of
NVECT_2month2 month animal · Adult tissues/organs1,61423not in this dataset–
NVECT_bodywallbody wall with mesenteries · 6-8 weeks adults11,74213not in this dataset–
NVECT_embryoembryos · 8, 10 and 12 h after fertilisation (deposit labels 8h/10h/12h)9,71117not in this dataset–
NVECT_gastrulaBlastula-gastrula intermediate · Developmental stages49,16627not in this dataset–
NVECT_gastruloiddissociated and reaggregated embryos · 4-48 hpa36,5508not in this dataset–
NVECT_neoplasmneoplasm · Adult tissues/organs2,53216not in this dataset–
NVECT_nervousGastrula Cells · nervous system16,59027unmapped–
NVECT_notch48hembryos treated 24-48 hpf (DMSO vs LY411575) · 48 hpf19,0447not in this dataset–
NVECT_tentacletentacle · Adult tissues/organs7,97719not in this dataset–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

Peak calls overlapping this gene

AssaySamplePeaksRegion
ChIP-seqH3K27ac_Ncol3_negative1Promoter (<=1kb) 1
H3K27ac_Ncol3_positive1Promoter (<=1kb) 1
H3K27ac_Nep3_negative1Promoter (<=1kb) 1
H3K36me3_planulae_4days4Promoter (<=1kb) 1 · Promoter (1-2kb) 1 · Promoter (2-3kb) 1 · Intron 1
H3K36me3_polyps4Promoter (<=1kb) 1 · Promoter (1-2kb) 1 · Promoter (2-3kb) 1 · Exon 1
H3K4me1_planulae_4days1Promoter (<=1kb) 1
H3K4me2_neuronal_ELAV_cells1Promoter (<=1kb) 1
late_gastrula2Promoter (<=1kb) 1 · Intron 1

Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.

DNA methylation (bisulphite samples)

SampleMethylation profile
Whole_adultsopen

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.template foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.open →
Gene set analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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