Detailed information of HSymV2.0_g14.24634_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_14:15577529...15599326
NR annotation: XP_047146744.1, E3 ubiquitin-protein ligase RAD18 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
Q9NS91E3 ubiquitin-protein ligase RAD18 OS=Homo sapiens OX=9606 GN=RAD18 PE=1 SV=2
Q9QXK2E3 ubiquitin-protein ligase RAD18 OS=Mus musculus OX=10090 GN=Rad18 PE=1 SV=2
O74747Postreplication repair E3 ubiquitin-protein ligase rad18 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=rhp18 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004614 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02037
all species →		SAPSAP domainDomainInterproscan
PF00097
all species →		zf-C3HC4Zinc finger, C3HC4 type (RING finger)DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR003034
all species →		DomainSAP domainInterproscan
IPR017907
all species →		Conserved_siteZinc finger, RING-type, conserved siteInterproscan
IPR006642
all species →		DomainRad18, zinc finger UBZ4-typeInterproscan
IPR039577
all species →		FamilyE3 ubiquitin-protein ligase Rad18Interproscan
IPR001841
all species →		DomainZinc finger, RING-typeInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR036361
all species →		Homologous_superfamilySAP domain superfamilyInterproscan
IPR018957
all species →		DomainZinc finger, C3HC4 RING-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14134
all species →		E3 UBIQUITIN-PROTEIN LIGASE RAD18Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0006281
all species →		Biological ProcessDNA repairInterproscan
GO:0003697
all species →		Molecular Functionsingle-stranded DNA bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006301
all species →		Biological Processpostreplication repairInterproscan
GO:0006513
all species →		Biological Processprotein monoubiquitinationInterproscan
GO:0061630
all species →		Molecular Functionubiquitin protein ligase activityInterproscan
GO:0097505
all species →		Cellular ComponentRad6-Rad18 complexInterproscan
GO:0046872
all species →		Molecular Functionmetal ion bindingInterproscan

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
K10627RAD18; E3 ubiquitin-protein ligase RAD18EC:2.3.2.27
DNA repair and recombination proteinsko03400deepkoala

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_g14.24634_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
62.1Max TPM
41.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 40.28 57.01
Whole embryo · Triptolide 20 uM 4 4 51.68 62.08
Whole embryo · DMSO 0.5% 4 4 36.25 46.26

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 57.01
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 56.36
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 55.67
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 55.02
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 54.03
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 53.87
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 52.31
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 52.30
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 52.04
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 51.69
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 51.43
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 50.92
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 50.72
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 49.96
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 48.66
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 48.42
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 47.97
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 47.80
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 47.52
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 47.31
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 46.91
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 46.76
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 46.75
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 44.08
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 43.02
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 42.43
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 38.37
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 30.99
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 28.40
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 20.14
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 7.04
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 6.43
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 5.81
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 5.16
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 4.81
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 2.08
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 62.08
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 56.49
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 47.33
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 40.81
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 46.26
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 43.74
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 30.71
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 24.27

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 correlated42HSymV2.0_g08.12842_t10.975746400970385
Negatively correlated42HSymV2.0_g09.16523_t1-0.952569783167807

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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