Detailed information of HSymV2.0_g05.09370_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_5:24036587...24045501
NR annotation: XP_002165851.1, uncharacterized protein LOC100198679 isoform X1 [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
A0JPN4Endoribonuclease ZC3H12A OS=Rattus norvegicus OX=10116 GN=Zc3h12a PE=2 SV=1
Q5D1E8Endoribonuclease ZC3H12A OS=Homo sapiens OX=9606 GN=ZC3H12A PE=1 SV=1
Q5D1E7Endoribonuclease ZC3H12A OS=Mus musculus OX=10090 GN=Zc3h12a PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001622 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF18039
all species →		UBA_6UBA-like domainDomainInterproscan
PF11977
all species →		RNase_Zc3h12aZc3h12a-like Ribonuclease NYN domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR040546
all species →		DomainRege-1, UBA-like domainInterproscan
IPR021869
all species →		DomainRibonuclease Zc3h12a-like, NYN domainInterproscan
IPR036612
all species →		Homologous_superfamilyK Homology domain, type 1 superfamilyInterproscan
IPR000571
all species →		DomainZinc finger, CCCH-typeInterproscan
IPR051101
all species →		FamilyZC3H12/N4BP1 Ribonuclease and RegulatorInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12876
all species →		N4BP1-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0046872
all species →		Molecular Functionmetal ion bindingInterproscan
GO:0003729
all species →		Molecular FunctionmRNA bindingInterproscan
GO:0004521
all species →		Molecular FunctionRNA endonuclease activityInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0036464
all species →		Cellular Componentcytoplasmic ribonucleoprotein granuleInterproscan
GO:0090502
all species →		Biological Processobsolete RNA phosphodiester bond hydrolysis, endonucleolyticInterproscan

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_g05.09370_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_g05.09370_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
139.8Max TPM
97.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 92.95 139.81
Whole embryo · Triptolide 20 uM 4 4 125.11 127.85
Whole embryo · DMSO 0.5% 4 4 114.77 127.50

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 139.81
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 131.02
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 125.72
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 123.35
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 120.30
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 118.40
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 115.66
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 114.15
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 114.01
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 112.55
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 112.54
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 112.14
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 111.01
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 110.44
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 108.94
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 107.05
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 104.22
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 103.24
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 101.79
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 101.02
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 99.23
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 99.11
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 99.07
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 98.85
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 98.40
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 97.64
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 95.16
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 94.66
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 94.07
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 90.45
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 26.78
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 19.18
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 19.04
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 9.74
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 9.62
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 7.99
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 127.85
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 126.01
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 124.52
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 122.06
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 127.50
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 121.17
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 107.96
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 102.45

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 correlated30HSymV2.0_g04.07299_t10.969188490616945
Negatively correlated45HSymV2.0_g10.18279_t1-0.950143615215977

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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