Detailed information of HSymV2.0_g05.09134_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_5:20886561...20917932
NR annotation: XP_047129251.1, tudor domain-containing protein 1 [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
Q4R3G4RING finger protein 17 OS=Macaca fascicularis OX=9541 GN=RNF17 PE=2 SV=2
Q9BXT8RING finger protein 17 OS=Homo sapiens OX=9606 GN=RNF17 PE=1 SV=3
Q99MV7RING finger protein 17 OS=Mus musculus OX=10090 GN=Rnf17 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003116 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13445
all species →		zf-RING_UBOXRING-type zinc-fingerDomainInterproscan
PF00567
all species →		TUDORTudor domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR035437
all species →		Homologous_superfamilySNase-like, OB-fold superfamilyInterproscan
IPR039117
all species →		FamilyRING finger protein 17Interproscan
IPR027370
all species →		DomainZinc finger, RING-type, eukaryoticInterproscan
IPR002999
all species →		DomainTudor domainInterproscan
IPR000315
all species →		DomainB-box-type zinc fingerInterproscan
IPR001841
all species →		DomainZinc finger, RING-typeInterproscan
IPR017907
all species →		Conserved_siteZinc finger, RING-type, conserved siteInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR16442
all species →		RING FINGER PROTEIN 17Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0008270
all species →		Molecular Functionzinc 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
K18405TDRD1_4_6_7; tudor domain-containing protein 1/4/6/7-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_g05.09134_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
43TPM > 0
3Conditions
53.9Max TPM
24.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 26.47 53.89
Whole embryo · Triptolide 20 uM 4 3 21.65 41.31
Whole embryo · DMSO 0.5% 4 4 12.71 22.57

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 53.89
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 53.28
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 51.97
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 50.83
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 49.92
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 49.66
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 49.58
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 48.78
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 48.56
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 47.56
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 46.18
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 45.75
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 44.87
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 33.75
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 22.74
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 20.83
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 19.01
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 18.34
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 18.22
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 17.96
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 17.51
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 16.50
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 15.80
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 15.60
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 15.59
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 13.06
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 12.51
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 8.99
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 8.03
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 7.01
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 6.99
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 6.26
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 5.17
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 4.85
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 3.77
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 3.54
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 41.31
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 40.62
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 4.66
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 0.00
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 22.57
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 20.41
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 4.18
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 3.70

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 correlated35HSymV2.0_g01.00905_t10.991029680500332
Negatively correlated12HSymV2.0_g11.19702_t1-0.928877774543851

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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