Detailed information of HSymV2.0_g12.21722_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_12:19119471...19127902
NR annotation: XP_047136982.1, 26S proteasome non-ATPase regulatory subunit 11 [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
F6P3G426S proteasome non-ATPase regulatory subunit 11A OS=Danio rerio OX=7955 GN=psmd11a PE=2 SV=1
F6XBL226S proteasome non-ATPase regulatory subunit 11 OS=Xenopus tropicalis OX=8364 GN=psmd11 PE=3 SV=2
Q2KI4226S proteasome non-ATPase regulatory subunit 11 OS=Bos taurus OX=9913 GN=PSMD11 PE=2 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005545 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01399
all species →		PCIPCI domainDomainInterproscan
PF18055
all species →		RPN6_N26S proteasome regulatory subunit RPN6 N-terminal domainRepeatInterproscan
PF18503
all species →		RPN6_C_helix26S proteasome subunit RPN6 C-terminal helix domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR011990
all species →		Homologous_superfamilyTetratricopeptide-like helical domain superfamilyInterproscan
IPR000717
all species →		DomainProteasome component (PCI) domainInterproscan
IPR050871
all species →		Family26S Proteasome and COP9 Signalosome ComponentsInterproscan
IPR036390
all species →		Homologous_superfamilyWinged helix DNA-binding domain superfamilyInterproscan
IPR040773
all species →		Domain26S proteasome regulatory subunit Rpn6, N-terminalInterproscan
IPR040780
all species →		Domain6S proteasome subunit Rpn6, C-terminal helix domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10678
all species →		26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 11/COP9 SIGNALOSOME COMPLEX SUBUNIT 2Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0005198
all species →		Molecular Functionstructural molecule activityInterproscan
GO:0006511
all species →		Biological Processubiquitin-dependent protein catabolic processInterproscan
GO:0008541
all species →		Cellular Componentproteasome regulatory particle, lid subcomplexInterproscan

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
K03036PSMD11, RPN6; 26S proteasome regulatory subunit N6-Proteasomeko03051deepkoala

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_g12.21722_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
219.0Max TPM
132.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 126.16 218.97
Whole embryo · Triptolide 20 uM 4 4 157.03 202.22
Whole embryo · DMSO 0.5% 4 4 167.72 202.07

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 218.97
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 192.54
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 182.26
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 172.68
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 151.44
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 149.79
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 148.88
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 144.56
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 139.22
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 138.85
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 137.01
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 136.32
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 135.83
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 134.87
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 134.28
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 131.08
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 127.38
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 127.28
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 127.14
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 125.49
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 123.55
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 122.94
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 111.25
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 107.42
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 105.86
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 101.52
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 96.44
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 94.24
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 93.75
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 92.98
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 92.95
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 92.22
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 90.01
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 89.31
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 88.90
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 82.53
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 202.22
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 158.97
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 135.87
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 131.07
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 202.07
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 192.79
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 140.68
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 135.35

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 correlated24HSymV2.0_g08.13201_t10.930447184092852
Negatively correlated44HSymV2.0_g12.21419_t1-0.860503637829595

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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