Detailed information of XP_048584158.1 in Nematostella vectensis

Genomic Location: NC_064034.1:5557520...5563049
NR annotation: XP_048584158.1, ubiquitin-like-conjugating enzyme ATG10 [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
Q9H0Y0Ubiquitin-like-conjugating enzyme ATG10 OS=Homo sapiens OX=9606 GN=ATG10 PE=1 SV=1
Q8R1P4Ubiquitin-like-conjugating enzyme ATG10 OS=Mus musculus OX=10090 GN=Atg10 PE=1 SV=1
Q8VZ52Ubiquitin-like-conjugating enzyme ATG10 OS=Arabidopsis thaliana OX=3702 GN=ATG10 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007197 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03987
all species →		Autophagy_act_CAutophagocytosis associated protein, active-site domain DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR007135
all species →		FamilyUbiquitin-like-conjugating enzyme Atg3/Atg10Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14957
all species →		UBIQUITIN-LIKE-CONJUGATING ENZYME ATG10Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005622
all species →		Cellular Componentintracellular anatomical structureInterproscan
GO:0006497
all species →		Biological Processprotein lipidationInterproscan
GO:0016236
all species →		Biological ProcessmacroautophagyInterproscan
GO:0019777
all species →		Molecular FunctionAtg12 transferase activityInterproscan
GO:0032446
all species →		Biological Processprotein modification by small protein conjugationInterproscan
GO:0019787
all species →		Molecular Functionubiquitin-like protein transferase activityInterproscan

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
K17888ATG10L, ATG10; ubiquitin-like-conjugating enzyme ATG10-Mitochondrial biogenesisko03029deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_048584158.1 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
39TPM > 0
16Conditions
1,038.4Max TPM
210.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole 6 week old aboral regenerate · regenerate 96hpa 3 3 340.81 651.61
whole 6 week old aboral regenerate · regenerate 144hpa 3 3 188.74 241.83
whole 6 week old aboral regenerate · regenerate 0hpa 3 3 256.79 307.47
whole 6 week old aboral regenerate · regenerate 2hpa 3 3 240.07 299.68
whole 6 week old aboral regenerate · regenerate uncut 3 3 230.90 296.03
whole 6 week old aboral regenerate · regenerate 4hpa 3 1 89.53 268.58
whole 6 week old aboral regenerate · regenerate 120hpa 3 2 117.93 215.00
whole 6 week old aboral regenerate · regenerate 36hpa 3 3 214.24 256.98
whole 6 week old aboral regenerate · regenerate 24hpa 3 2 128.65 232.35
whole 6 week old aboral regenerate · regenerate 20hpa 3 2 121.74 236.07
whole 6 week old aboral regenerate · regenerate 16hpa 3 3 229.48 271.86
whole 6 week old aboral regenerate · regenerate 72hpa 3 2 149.70 226.89
whole 6 week old aboral regenerate · regenerate 60hpa 3 3 208.60 249.03
whole 6 week old aboral regenerate · regenerate 48hpa 3 2 298.25 755.02
whole 6 week old aboral regenerate · regenerate 8hpa 3 3 491.75 1,038.43
whole 6 week old aboral regenerate · regenerate 12hpa 3 1 53.08 159.25

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR6320837 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 651.61
SRR6320836 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 223.93
SRR6320863 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 146.89
SRR6320838 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 241.83
SRR6320841 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 184.70
SRR6320847 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 139.69
SRR6320840 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 307.47
SRR6320839 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 291.27
SRR6320846 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 171.62
SRR6320848 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 299.68
SRR6320842 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 261.56
SRR6320861 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 158.95
SRR6320845 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 296.03
SRR6320844 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 233.34
SRR6320843 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 163.32
SRR6320872 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 268.58
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
SRR6320883 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 215.00
SRR6320882 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 138.78
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 256.98
SRR6320852 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 229.03
SRR6320855 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 156.71
SRR6320853 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 232.35
SRR6320854 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 153.61
SRR6320856 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 0.00
SRR6320860 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 236.07
SRR6320857 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 129.16
SRR6320859 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 0.00
SRR6320858 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 271.86
SRR6320881 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 261.22
SRR6320880 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 155.37
SRR6320862 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 226.89
SRR6320865 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 222.21
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 249.03
SRR6320866 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 228.31
SRR6320869 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 148.45
SRR6320871 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 755.02
SRR6320870 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 139.75
SRR6320868 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 0.00
SRR6320876 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 1,038.43
SRR6320875 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 271.34
SRR6320874 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 165.50
SRR6320877 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 159.25
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 correlated8XP_001640346.10.768637040503161
Negatively correlated27XP_048589299.1-0.663121323589372

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_gastrulae_24h1Promoter (<=1kb) 1
H3K4me2_gastrulae_24h1Promoter (<=1kb) 1
H3K4me2_polyps1Promoter (<=1kb) 1
H3K36me3_gastrulae_24h1Promoter (1-2kb) 1
H3K36me3_planulae_4days2Promoter (<=1kb) 2
H3K36me3_polyps1Promoter (<=1kb) 1
H3K4me1_planulae_4days1Promoter (<=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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