Detailed information of XP_001639141.2 in Nematostella vectensis

Genomic Location: NC_064043.1:11103415...11105905
NR annotation: XP_001639141.2, ubiquitin-fold modifier 1 [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
Q5RJW4Ubiquitin-fold modifier 1 OS=Xenopus laevis OX=8355 GN=ufm1 PE=3 SV=1
B3DL37Ubiquitin-fold modifier 1 OS=Xenopus tropicalis OX=8364 GN=ufm1 PE=3 SV=1
Q5BJP3Ubiquitin-fold modifier 1 OS=Rattus norvegicus OX=10116 GN=Ufm1 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0009156 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03671
all species →		Ufm1Ubiquitin fold modifier 1 proteinDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR005375
all species →		FamilyUbiquitin-fold modifier 1Interproscan
IPR029071
all species →		Homologous_superfamilyUbiquitin-like domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR15825
all species →		UBIQUITIN-FOLD MODIFIER 1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0071569
all species →		Biological Processprotein ufmylationInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:1990592
all species →		Biological Processprotein K69-linked ufmylationInterproscan

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
K12162UFM1; ubiquitin-fold modifier 1-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_001639141.2 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
48TPM > 0
16Conditions
271.9Max TPM
189.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole 6 week old aboral regenerate · regenerate 96hpa 3 3 192.86 221.46
whole 6 week old aboral regenerate · regenerate 144hpa 3 3 214.88 234.53
whole 6 week old aboral regenerate · regenerate 0hpa 3 3 177.90 184.14
whole 6 week old aboral regenerate · regenerate 2hpa 3 3 184.12 189.65
whole 6 week old aboral regenerate · regenerate uncut 3 3 189.14 206.86
whole 6 week old aboral regenerate · regenerate 4hpa 3 3 191.66 233.48
whole 6 week old aboral regenerate · regenerate 120hpa 3 3 231.98 271.86
whole 6 week old aboral regenerate · regenerate 36hpa 3 3 188.72 218.04
whole 6 week old aboral regenerate · regenerate 24hpa 3 3 169.07 188.93
whole 6 week old aboral regenerate · regenerate 20hpa 3 3 171.31 176.33
whole 6 week old aboral regenerate · regenerate 16hpa 3 3 183.37 189.53
whole 6 week old aboral regenerate · regenerate 72hpa 3 3 187.81 195.82
whole 6 week old aboral regenerate · regenerate 60hpa 3 3 209.96 265.15
whole 6 week old aboral regenerate · regenerate 48hpa 3 3 202.38 225.70
whole 6 week old aboral regenerate · regenerate 8hpa 3 3 170.35 177.04
whole 6 week old aboral regenerate · regenerate 12hpa 3 3 166.96 200.29

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR6320863 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 221.46
SRR6320836 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 188.82
SRR6320837 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 168.32
SRR6320847 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 234.53
SRR6320838 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 221.19
SRR6320841 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 188.90
SRR6320846 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 184.14
SRR6320839 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 180.53
SRR6320840 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 169.02
SRR6320842 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 189.65
SRR6320848 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 183.52
SRR6320861 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 179.20
SRR6320845 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 206.86
SRR6320843 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 195.12
SRR6320844 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 165.43
SRR6320849 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 233.48
SRR6320872 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 174.81
SRR6320873 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 166.70
SRR6320850 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 271.86
SRR6320883 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 215.54
SRR6320882 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 208.54
SRR6320855 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 218.04
SRR6320851 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 181.19
SRR6320852 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 166.92
SRR6320854 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 188.93
SRR6320853 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 175.53
SRR6320856 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 142.74
SRR6320857 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 176.33
SRR6320860 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 172.27
SRR6320859 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 165.33
SRR6320880 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 189.53
SRR6320881 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 185.39
SRR6320858 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 175.18
SRR6320864 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 195.82
SRR6320862 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 193.83
SRR6320865 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 173.79
SRR6320869 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 265.15
SRR6320867 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 190.59
SRR6320866 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 174.14
SRR6320868 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 225.70
SRR6320871 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 203.11
SRR6320870 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 178.33
SRR6320874 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 177.04
SRR6320875 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 167.02
SRR6320876 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 167.00
SRR6320878 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 200.29
SRR6320877 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 178.45
SRR6320879 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 122.14

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 correlated1XP_001624116.20.710234308207089
Negatively correlated15XP_001624813.3-0.63862495966834

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/organs2,53216in viewerCluster 14 (2.501, 0.333%)
Cluster 15 (3.273, 0.417%)
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/organs7,97719in viewerCluster 12 (2.474, 0.533%)

Opening a dataset shows the UMAP with this gene coloured and the violin plot of its expression per cell type. 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_gastrulae_24h1Promoter (<=1kb) 1
H3K27ac_planulae_4days2Promoter (<=1kb) 1 · Promoter (1-2kb) 1
H3K4me2_gastrulae_24h1Promoter (<=1kb) 1
H3K4me2_planulae_4days1Promoter (<=1kb) 1
H3K4me2_polyps2Promoter (<=1kb) 2
H3K4me3_gastrulae_24h1Promoter (<=1kb) 1
H3K4me3_planulae_4days1Promoter (<=1kb) 1
H3K4me3_polyps1Promoter (<=1kb) 1
H3K27ac_Ncol3_positive1Promoter (<=1kb) 1
H3K27ac_Nep3_positive1Promoter (<=1kb) 1
H3K36me3_planulae_4days1Promoter (<=1kb) 1
H3K4me1_gastrulae_24h2Promoter (<=1kb) 2
H3K4me1_planulae_4days4Promoter (<=1kb) 3 · Promoter (1-2kb) 1
H3K4me2_neuronal_ELAV_cells1Promoter (<=1kb) 1
H3K4me3_neuronal_ELAV_cells1Promoter (<=1kb) 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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