Detailed information of XP_066913851.1 in Clytia hemisphaerica

Genomic Location: NW_027103573.1:130503...140883
NR annotation: XP_047142271.1, ribosomal RNA small subunit methyltransferase NEP1 [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
O35130Ribosomal RNA small subunit methyltransferase NEP1 OS=Mus musculus OX=10090 GN=Emg1 PE=1 SV=1
Q92979Ribosomal RNA small subunit methyltransferase NEP1 OS=Homo sapiens OX=9606 GN=EMG1 PE=1 SV=4
Q9W4J5Ribosomal RNA small subunit methyltransferase NEP1 OS=Drosophila melanogaster OX=7227 GN=CG3527 PE=3 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006715 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03587
all species →		EMG1EMG1/NEP1 methyltransferaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR005304
all species →		FamilyRibosomal biogenesis, methyltransferase, EMG1/NEP1Interproscan
IPR029026
all species →		Homologous_superfamilytRNA (guanine-N1-)-methyltransferase, N-terminalInterproscan
IPR029028
all species →		Homologous_superfamilyAlpha/beta knot methyltransferasesInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12636
all species →		NEP1/MRA1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005730
all species →		Cellular ComponentnucleolusInterproscan
GO:0019843
all species →		Molecular FunctionrRNA bindingInterproscan
GO:0032040
all species →		Cellular Componentsmall-subunit processomeInterproscan
GO:0070037
all species →		Molecular FunctionrRNA (pseudouridine) methyltransferase activityInterproscan
GO:0070475
all species →		Biological ProcessrRNA base methylationInterproscan

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
K14568EMG1, NEP1; rRNA small subunit pseudouridine methyltransferase Nep1EC:2.1.1.260
Ribosome biogenesisko03009deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_066913851.1 across 40 RNA-seq samples of Clytia hemisphaerica. 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.

40Samples
36TPM > 0
16Conditions
58.0Max TPM
26.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Mature medusa 5 5 46.39 58.03
medusa · Experiment Condition A1 4 4 29.84 30.58
medusa · Experiment Condition A2 4 4 10.04 11.33
medusa · Experiment Condition A3 4 0 0.00 0.00
Early gastrula 2 2 39.63 40.00
Planula 24hpf 2 2 37.01 38.58
Planula 48hpf 2 2 29.94 30.80
Planula 72hpf 2 2 26.47 27.26
Primary polyp 2 2 34.88 39.08
Gastrozooid 2 2 7.46 8.32
Gonozooid 2 2 29.32 29.61
Stolon 2 2 28.55 30.63
Baby medusa 2 2 32.54 35.11
medusa · Experiment Condition B1 2 2 20.01 20.01
medusa · Experiment Condition B2 2 2 29.99 30.14
Mixed 1 1 32.41 32.41

Per sample · hover a bar for the full sample record

Show the sample table (40 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR2862245 Mature medusa not recorded Mature medusa not recorded ERP110164 58.03
ERR2816251 Mature medusa not recorded Mature medusa not recorded ERP110164 51.57
ERR2816250 Mature medusa not recorded Mature medusa not recorded ERP110164 49.18
ERR2816248 Mature medusa not recorded Mature medusa not recorded ERP110164 40.14
ERR2816249 Mature medusa not recorded Mature medusa not recorded ERP110164 33.01
ERR3299475 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 30.58
ERR3299477 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 30.16
ERR3299478 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 29.38
ERR3299476 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 29.26
ERR3299480 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 11.33
ERR3299481 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 10.81
ERR3299482 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 9.56
ERR3299479 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 8.45
ERR3299483 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 0.00
ERR3299484 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 0.00
ERR3299485 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 0.00
ERR3299486 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 0.00
ERR2816230 Early gastrula not recorded Early gastrula not recorded ERP110164 40.00
ERR2816231 Early gastrula not recorded Early gastrula not recorded ERP110164 39.25
ERR2816233 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 38.58
ERR2816232 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 35.44
ERR2816235 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 30.80
ERR2816234 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 29.08
ERR2816237 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 27.26
ERR2816236 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 25.68
ERR2816239 Primary polyp not recorded Primary polyp not recorded ERP110164 39.08
ERR2816238 Primary polyp not recorded Primary polyp not recorded ERP110164 30.69
ERR2816241 Gastrozooid not recorded Gastrozooid not recorded ERP110164 8.32
ERR2816240 Gastrozooid not recorded Gastrozooid not recorded ERP110164 6.60
ERR2816242 Gonozooid not recorded Gonozooid not recorded ERP110164 29.61
ERR2816243 Gonozooid not recorded Gonozooid not recorded ERP110164 29.03
ERR2816245 Stolon not recorded Stolon not recorded ERP110164 30.63
ERR2816244 Stolon not recorded Stolon not recorded ERP110164 26.47
ERR2816246 Baby medusa not recorded Baby medusa not recorded ERP110164 35.11
ERR2816247 Baby medusa not recorded Baby medusa not recorded ERP110164 29.96
ERR3299472 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 20.01
ERR3299471 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 20.00
ERR3299474 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 30.14
ERR3299473 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 29.83
ERR2862244 Mixed not recorded Mixed not recorded ERP110164 32.41

Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM, StringTie quantification over 40 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 Clytia hemisphaerica 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 correlated33XP_066918562.10.939123128646295
Negatively correlated26XP_066931915.1-0.848851206337423

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 Clytia hemisphaerica, 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.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

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.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

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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