Detailed information of HSymV2.0_g01.00824_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_1:14553082...14554290
NR annotation: XP_004206439.2, TIMELESS-interacting protein [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)
No Swiss-Prot hit above the reporting threshold for this gene.
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006951 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF07962
all species →		Swi3Replication Fork Protection Component Swi3FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR040038
all species →		FamilyTIPIN/Csm3/Swi3Interproscan
IPR012923
all species →		DomainChromosome segregation in meiosis protein 3Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13220
all species →		TIMELESS INTERACTING-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000076
all species →		Biological ProcessDNA replication checkpoint signalingInterproscan
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0031298
all species →		Cellular Componentreplication fork protection complexInterproscan
GO:0043111
all species →		Biological Processreplication fork arrestInterproscan
GO:0048478
all species →		Biological Processobsolete replication fork protectionInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006974
all species →		Biological ProcessDNA damage responseInterproscan
GO:0031297
all species →		Biological Processreplication fork processingInterproscan

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
K10998TIPIN, CSM3, SWI3; replication fork protection complex subunit TIPIN/Csm3/Swi3-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_g01.00824_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
134.2Max TPM
79.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 75.55 120.99
Whole embryo · Triptolide 20 uM 4 4 104.68 134.18
Whole embryo · DMSO 0.5% 4 4 85.40 98.46

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 120.99
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 111.56
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 105.18
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 103.82
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 103.59
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 102.60
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 98.81
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 97.73
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 96.10
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 94.05
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 92.82
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 92.71
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 92.66
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 91.58
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 88.57
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 84.77
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 82.42
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 82.24
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 80.73
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 80.02
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 79.63
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 78.18
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 77.25
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 76.20
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 75.23
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 72.18
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 71.98
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 70.76
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 70.38
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 66.81
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 23.19
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 19.50
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 10.52
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 9.50
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 9.26
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 6.13
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 134.18
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 114.92
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 87.13
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 82.50
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 98.46
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 97.58
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 73.63
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 71.94

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 correlated36HSymV2.0_g01.01088_t10.983015169993701
Negatively correlated7HSymV2.0_g09.16502_t1-0.899402349244085

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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