Detailed information of HSymV2.0_g08.14604_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_8:26555147...26560373
NR annotation: XP_045164471.2, serine-rich adhesin for platelets-like isoform X1 [Mercenaria mercenaria]
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)OG0004159 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF05454
all species →		DAG1Dystroglycan (Dystrophin-associated glycoprotein 1)FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR013783
all species →		Homologous_superfamilyImmunoglobulin-like foldInterproscan
IPR008465
all species →		DomainDystroglycan, C-terminalInterproscan
IPR030398
all species →		DomainDG-type SEA domainInterproscan
IPR015919
all species →		Homologous_superfamilyCadherin-like superfamilyInterproscan
IPR006644
all species →		DomainDystroglycan-type cadherin-likeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR21559
all species →		DYSTROGLYCAN-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0016010
all species →		Cellular Componentdystrophin-associated glycoprotein complexInterproscan
GO:0002009
all species →		Biological Processmorphogenesis of an epitheliumInterproscan
GO:0007411
all species →		Biological Processaxon guidanceInterproscan
GO:0016011
all species →		Cellular Componentdystroglycan complexInterproscan
GO:0016203
all species →		Biological Processmuscle attachmentInterproscan
GO:0021675
all species →		Biological Processnerve developmentInterproscan
GO:0042383
all species →		Cellular ComponentsarcolemmaInterproscan
GO:0043236
all species →		Molecular Functionlaminin bindingInterproscan
GO:0005509
all species →		Molecular Functioncalcium ion bindingInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan

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_g08.14604_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_g08.14604_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
62.0Max TPM
26.2Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 25.91 61.96
Whole embryo · Triptolide 20 uM 4 4 29.26 49.72
Whole embryo · DMSO 0.5% 4 4 25.69 43.76

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 61.96
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 55.83
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 51.59
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 48.44
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 47.37
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 46.77
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 44.91
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 39.26
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 32.60
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 32.09
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 30.00
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 29.15
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 28.86
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 26.90
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 25.64
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 25.17
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 25.01
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 24.55
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 24.19
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 23.88
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 22.77
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 20.29
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 17.38
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 17.16
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 16.73
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 16.53
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 16.24
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 15.71
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 13.91
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 12.33
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 11.70
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 11.08
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 7.20
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 5.12
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 2.68
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 1.91
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 49.72
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 46.07
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 10.73
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 10.53
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 43.76
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 38.75
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 11.08
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 9.18

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 correlated17HSymV2.0_g10.18304_t10.951666763536614
Negatively correlated17HSymV2.0_g02.03357_t1-0.902917872533242

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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