Detailed information of HSymV2.0_g15.24959_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_15:637704...654319
NR annotation: XP_047124778.1, double-strand-break repair protein rad21 homolog 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)
No Swiss-Prot hit above the reporting threshold for this gene.
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006802 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF04825
all species →		Rad21_Rec8_NN terminus of Rad21 / Rec8 like proteinFamilyInterproscan
PF04824
all species →		Rad21_Rec8Conserved region of Rad21 / Rec8 like proteinFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036390
all species →		Homologous_superfamilyWinged helix DNA-binding domain superfamilyInterproscan
IPR039781
all species →		FamilyRad21/Rec8-like proteinInterproscan
IPR023093
all species →		Homologous_superfamilyScpA-like, C-terminalInterproscan
IPR006910
all species →		DomainRad21/Rec8-like protein, N-terminalInterproscan
IPR006909
all species →		DomainRad21/Rec8-like protein, C-terminal, eukaryoticInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12585
all species →		SCC1 / RAD21 FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003682
all species →		Molecular Functionchromatin bindingInterproscan
GO:0007062
all species →		Biological Processsister chromatid cohesionInterproscan
GO:0008278
all species →		Cellular Componentcohesin complexInterproscan
GO:0034991
all species →		Cellular Componentmeiotic cohesin complexInterproscan
GO:1990414
all species →		Biological Processreplication-born double-strand break repair via sister chromatid exchangeInterproscan
GO:0005515
all species →		Molecular Functionprotein 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
No KEGG orthology assignment for HSymV2.0_g15.24959_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_g15.24959_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
82.1Max TPM
36.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 42.92 82.12
Whole embryo · Triptolide 20 uM 4 3 8.19 15.72
Whole embryo · DMSO 0.5% 4 4 9.58 13.63

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 82.12
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 81.50
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 79.36
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 78.47
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 78.26
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 76.98
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 74.80
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 73.39
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 72.22
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 69.17
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 68.10
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 65.21
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 57.53
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 56.55
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 55.01
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 49.74
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 46.06
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 45.31
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 41.22
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 31.24
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 30.98
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 29.30
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 28.07
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 24.08
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 23.11
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 19.36
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 17.39
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 14.36
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 12.63
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 12.03
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 9.98
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 9.39
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 9.29
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 9.18
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 7.53
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 6.26
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 15.72
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 14.93
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 2.12
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 0.00
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 13.63
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 12.18
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 6.64
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 5.85

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 correlated39HSymV2.0_g10.18652_t10.985189544823148
Negatively correlated3HSymV2.0_g14.24097_t1-0.838665245800037

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