Detailed information of HSymV2.0_g07.12017_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_7:11496820...11521314
NR annotation: XP_047143819.1, 18S rRNA aminocarboxypropyltransferase [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
Q9UJK018S rRNA aminocarboxypropyltransferase OS=Homo sapiens OX=9606 GN=TSR3 PE=1 SV=1
Q5HZH218S rRNA aminocarboxypropyltransferase OS=Mus musculus OX=10090 GN=Tsr3 PE=1 SV=1
Q1040918S rRNA aminocarboxypropyltransferase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=tsr3 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005170 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF04068
all species →		RLIPossible Fer4-like domain in RNase L inhibitor, RLIFamilyInterproscan
PF04034
all species →		Ribo_biogen_CRibosome biogenesis protein, C-terminalDomainInterproscan
PF02755
all species →		RPELRPEL repeatDisorderedInterproscan
PF02037
all species →		SAPSAP domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR004018
all species →		RepeatRPEL repeatInterproscan
IPR007209
all species →		DomainRNase L inhibitor RLI-like, possible metal-binding domainInterproscan
IPR022968
all species →		Family16S/18S rRNA aminocarboxypropyltransferase Tsr3Interproscan
IPR036361
all species →		Homologous_superfamilySAP domain superfamilyInterproscan
IPR003034
all species →		DomainSAP domainInterproscan
IPR007177
all species →		Domain16S/18S rRNA aminocarboxypropyltransferase Tsr3, C-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR20426
all species →		RIBOSOME BIOGENESIS PROTEIN TSR3 HOMOLOGInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006364
all species →		Biological ProcessrRNA processingInterproscan
GO:0016740
all species →		Molecular Functiontransferase activityInterproscan
GO:0106388
all species →		Molecular Function18S rRNA aminocarboxypropyltransferase activityInterproscan
GO:0030490
all species →		Biological Processmaturation of SSU-rRNAInterproscan

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_g07.12017_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_g07.12017_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
208.3Max TPM
90.2Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 98.33 208.33
Whole embryo · Triptolide 20 uM 4 4 47.51 64.06
Whole embryo · DMSO 0.5% 4 4 59.39 76.36

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 208.33
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 182.95
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 182.32
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 181.15
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 168.66
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 153.73
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 144.49
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 143.98
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 141.08
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 136.28
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 135.82
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 130.83
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 128.21
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 114.03
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 113.69
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 105.09
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 102.12
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 100.10
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 100.04
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 89.81
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 87.89
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 83.78
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 76.37
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 75.98
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 75.10
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 66.43
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 56.43
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 50.49
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 49.41
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 45.58
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 24.57
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 21.77
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 20.15
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 18.75
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 13.27
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 11.20
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 64.06
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 64.05
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 33.11
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 28.82
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 76.36
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 68.88
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 46.71
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 45.63

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 correlated34HSymV2.0_g07.11535_t10.974431491983102
Negatively correlated4HSymV2.0_g04.07169_t1-0.850490022414917

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 →
TOP