Detailed information of HSymV2.0_g03.05500_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_3:23959816...23978450
NR annotation: XP_002165955.2, serum paraoxonase/arylesterase 1-like [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
Q04688DNA-binding protein Ets97D OS=Drosophila melanogaster OX=7227 GN=Ets97D PE=1 SV=2
Q00422GA-binding protein alpha chain OS=Mus musculus OX=10090 GN=Gabpa PE=1 SV=2
P81270Transcriptional regulator ERG OS=Mus musculus OX=10090 GN=Erg PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002134 (this species only) · gene tree & orthology
Transcription factor familyETS · all TF in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00178
all species →		EtsEts-domainDomainInterproscan
PF02198
all species →		SAM_PNTSterile alpha motif (SAM)/Pointed domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000418
all species →		DomainEts domainInterproscan
IPR036388
all species →		Homologous_superfamilyWinged helix-like DNA-binding domain superfamilyInterproscan
IPR036390
all species →		Homologous_superfamilyWinged helix DNA-binding domain superfamilyInterproscan
IPR011042
all species →		Homologous_superfamilySix-bladed beta-propeller, TolB-likeInterproscan
IPR002640
all species →		FamilyArylesteraseInterproscan
IPR003118
all species →		DomainPointed domainInterproscan
IPR013761
all species →		Homologous_superfamilySterile alpha motif/pointed domain superfamilyInterproscan
IPR051288
all species →		FamilySerum paraoxonase/arylesteraseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11799
all species →		PARAOXONASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003700
all species →		Molecular FunctionDNA-binding transcription factor activityInterproscan
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0043565
all species →		Molecular Functionsequence-specific DNA bindingInterproscan
GO:0004064
all species →		Molecular Functionarylesterase 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
No KEGG orthology assignment for HSymV2.0_g03.05500_t1.

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_g03.05500_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
85.6Max TPM
43.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 47.80 85.62
Whole embryo · Triptolide 20 uM 4 4 25.55 34.08
Whole embryo · DMSO 0.5% 4 4 21.69 26.73

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 85.62
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 84.41
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 83.20
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 81.87
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 80.01
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 79.87
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 79.72
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 79.10
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 77.13
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 75.27
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 73.90
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 68.87
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 67.26
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 66.20
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 65.24
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 61.57
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 60.87
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 56.81
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 40.86
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 34.58
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 30.38
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 26.86
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 25.61
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 24.44
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 23.49
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 22.14
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 22.12
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 20.60
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 20.00
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 18.90
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 16.70
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 15.95
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 15.50
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 14.43
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 11.59
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 9.77
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 34.08
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 34.06
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 17.49
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 16.57
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 26.73
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 22.70
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 18.68
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 18.64

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_g10.18133_t10.982746284170719
Negatively correlated3HSymV2.0_g04.07015_t1-0.838701850248369

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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