Detailed information of XP_066929908.1 in Clytia hemisphaerica

Genomic Location: NW_027104306.1:26749...32363
NR annotation: XP_002156519.1, RNA demethylase ALKBH5 isoform X1 [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
E1BH29RNA demethylase ALKBH5 OS=Bos taurus OX=9913 GN=ALKBH5 PE=3 SV=1
Q6P6C2RNA demethylase ALKBH5 OS=Homo sapiens OX=9606 GN=ALKBH5 PE=1 SV=2
D3ZKD3RNA demethylase ALKBH5 OS=Rattus norvegicus OX=10116 GN=Alkbh5 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008303 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13532
all species →		2OG-FeII_Oxy_22OG-Fe(II) oxygenase superfamilyDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR027450
all species →		DomainAlpha-ketoglutarate-dependent dioxygenase AlkB-likeInterproscan
IPR037151
all species →		Homologous_superfamilyAlpha-ketoglutarate-dependent dioxygenase AlkB-like superfamilyInterproscan
IPR032860
all species →		FamilyRNA demethylase ALKBH5Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR32074
all species →		RNA DEMETHYLASE ALKBH5Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006397
all species →		Biological ProcessmRNA processingInterproscan
GO:0006406
all species →		Biological ProcessmRNA export from nucleusInterproscan
GO:0035515
all species →		Molecular Functionoxidative RNA demethylase activityInterproscan
GO:0035553
all species →		Biological Processobsolete oxidative single-stranded RNA demethylationInterproscan

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
K10767ALKBH5; mRNA N6-methyladenine demethylaseEC:1.14.11.53
Messenger RNA biogenesisko03019deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_066929908.1 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
40TPM > 0
16Conditions
49.1Max TPM
18.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Mature medusa 5 5 22.06 26.61
medusa · Experiment Condition A1 4 4 11.29 11.99
medusa · Experiment Condition A2 4 4 12.60 14.04
medusa · Experiment Condition A3 4 4 46.26 49.08
Early gastrula 2 2 16.78 18.46
Planula 24hpf 2 2 18.15 18.95
Planula 48hpf 2 2 17.02 18.73
Planula 72hpf 2 2 15.58 15.87
Primary polyp 2 2 12.41 14.77
Gastrozooid 2 2 14.89 17.19
Gonozooid 2 2 13.21 14.46
Stolon 2 2 10.00 10.46
Baby medusa 2 2 17.85 19.41
medusa · Experiment Condition B1 2 2 14.23 14.30
medusa · Experiment Condition B2 2 2 11.14 11.26
Mixed 1 1 16.97 16.97

Per sample · hover a bar for the full sample record

Show the sample table (40 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR2816248 Mature medusa not recorded Mature medusa not recorded ERP110164 26.61
ERR2816249 Mature medusa not recorded Mature medusa not recorded ERP110164 24.69
ERR2862245 Mature medusa not recorded Mature medusa not recorded ERP110164 23.43
ERR2816251 Mature medusa not recorded Mature medusa not recorded ERP110164 19.34
ERR2816250 Mature medusa not recorded Mature medusa not recorded ERP110164 16.21
ERR3299477 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 11.99
ERR3299476 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 11.58
ERR3299478 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 11.31
ERR3299475 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 10.28
ERR3299480 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 14.04
ERR3299479 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 13.52
ERR3299482 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 11.77
ERR3299481 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 11.08
ERR3299483 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 49.08
ERR3299484 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 46.68
ERR3299485 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 45.53
ERR3299486 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 43.77
ERR2816230 Early gastrula not recorded Early gastrula not recorded ERP110164 18.46
ERR2816231 Early gastrula not recorded Early gastrula not recorded ERP110164 15.10
ERR2816233 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 18.95
ERR2816232 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 17.35
ERR2816234 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 18.73
ERR2816235 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 15.31
ERR2816236 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 15.87
ERR2816237 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 15.28
ERR2816238 Primary polyp not recorded Primary polyp not recorded ERP110164 14.77
ERR2816239 Primary polyp not recorded Primary polyp not recorded ERP110164 10.06
ERR2816241 Gastrozooid not recorded Gastrozooid not recorded ERP110164 17.19
ERR2816240 Gastrozooid not recorded Gastrozooid not recorded ERP110164 12.59
ERR2816242 Gonozooid not recorded Gonozooid not recorded ERP110164 14.46
ERR2816243 Gonozooid not recorded Gonozooid not recorded ERP110164 11.96
ERR2816245 Stolon not recorded Stolon not recorded ERP110164 10.46
ERR2816244 Stolon not recorded Stolon not recorded ERP110164 9.53
ERR2816246 Baby medusa not recorded Baby medusa not recorded ERP110164 19.41
ERR2816247 Baby medusa not recorded Baby medusa not recorded ERP110164 16.29
ERR3299471 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 14.30
ERR3299472 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 14.17
ERR3299474 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 11.26
ERR3299473 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 11.03
ERR2862244 Mixed not recorded Mixed not recorded ERP110164 16.97

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 correlated12XP_066927193.10.954333593821905
Negatively correlated7XP_066930981.1-0.861816683912755

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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