Detailed information of HSymV2.0_g02.04125_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_2:30629638...30650357
NR annotation: XP_047146047.1, lysine-specific demethylase 4A isoform X3 [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9H3R0Lysine-specific demethylase 4C OS=Homo sapiens OX=9606 GN=KDM4C PE=1 SV=2
Q8VCD7Lysine-specific demethylase 4C OS=Mus musculus OX=10090 GN=Kdm4c PE=1 SV=1
Q8BW72Lysine-specific demethylase 4A OS=Mus musculus OX=10090 GN=Kdm4a PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006134 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02373
all species →		JmjCJmjC domain, hydroxylaseDomainInterproscan
PF02375
all species →		JmjNjmjN domainFamilyInterproscan
PF18104
all species →		Tudor_2Jumonji domain-containing protein 2A Tudor domainDomainInterproscan
PF13832
all species →		zf-HC5HC2H_2PHD-zinc-finger like domainDomainInterproscan
PF13831
all species →		PHD_2PHD-fingerFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001965
all species →		DomainZinc finger, PHD-typeInterproscan
IPR003349
all species →		DomainJmjN domainInterproscan
IPR003347
all species →		DomainJmjC domainInterproscan
IPR002999
all species →		DomainTudor domainInterproscan
IPR040477
all species →		DomainLysine-specific demethylase 4-like, Tudor domainInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR034732
all species →		DomainExtended PHD (ePHD) domainInterproscan
IPR011011
all species →		Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10694
all species →		LYSINE-SPECIFIC DEMETHYLASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000785
all species →		Cellular ComponentchromatinInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006338
all species →		Biological Processchromatin remodelingInterproscan
GO:0010468
all species →		Biological Processregulation of gene expressionInterproscan
GO:0032452
all species →		Molecular Functionhistone demethylase activityInterproscan
GO:0032454
all species →		Molecular Functionhistone H3K9 demethylase 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
K06709KDM4, JMJD2, JHDM3; [histone H3]-trimethyl-L-lysine9/36 demethylaseEC:1.14.11.66
EC:1.14.11.69
Chromosome and associated proteinsko03036deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of HSymV2.0_g02.04125_t1 across 44 RNA-seq samples of Hydractinia symbiolongicarpus. 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.

44Samples
44TPM > 0
3Conditions
126.3Max TPM
64.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 71.12 126.27
Whole embryo · Triptolide 20 uM 4 4 30.90 55.36
Whole embryo · DMSO 0.5% 4 4 33.12 48.59

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 126.27
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 125.58
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 121.94
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 121.62
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 120.80
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 120.66
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 120.37
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 117.97
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 115.31
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 114.49
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 113.36
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 112.64
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 112.11
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 108.12
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 104.42
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 92.90
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 90.98
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 85.27
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 77.34
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 58.25
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 42.11
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 37.43
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 32.87
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 30.29
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 28.95
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 26.89
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 25.91
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 24.73
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 24.17
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 21.78
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 20.32
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 20.17
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 19.57
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 18.91
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 15.32
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 10.36
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 55.36
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 50.69
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 10.49
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 7.05
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 48.59
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 43.81
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 20.15
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 19.95

Source: CnidoSite RNA-seq expression matrices (HSYMB_TPM, StringTie quantification over 44 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 Hydractinia symbiolongicarpus 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 correlated40HSymV2.0_g10.18404_t10.991632247022943
Negatively correlated3HSymV2.0_g14.24097_t1-0.822045204397579

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 Hydractinia symbiolongicarpus, 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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