Detailed information of HSymV2.0_g07.12004_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_7:11330673...11348759
NR annotation: XP_047142808.1, hepatocyte growth factor-regulated tyrosine kinase substrate isoform X2 [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
Q99LI8Hepatocyte growth factor-regulated tyrosine kinase substrate OS=Mus musculus OX=10090 GN=Hgs PE=1 SV=2
O14964Hepatocyte growth factor-regulated tyrosine kinase substrate OS=Homo sapiens OX=9606 GN=HGS PE=1 SV=1
Q0V8S0Hepatocyte growth factor-regulated tyrosine kinase substrate OS=Bos taurus OX=9913 GN=HGS PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003063 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF12210
all species →		Hrs_helicalHepatocyte growth factor-regulated tyrosine kinase substrateDomainInterproscan
PF00790
all species →		VHSVHS domainRepeatInterproscan
PF01363
all species →		FYVEFYVE zinc fingerDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR003903
all species →		Conserved_siteUbiquitin interacting motifInterproscan
IPR008942
all species →		Homologous_superfamilyENTH/VHSInterproscan
IPR011011
all species →		Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR002014
all species →		DomainVHS domainInterproscan
IPR017073
all species →		FamilyHepatocyte growth factor-regulated tyrosine kinase substrate/VPS27Interproscan
IPR024641
all species →		DomainHepatocyte growth factor-regulated tyrosine kinase substrate, helical domainInterproscan
IPR000306
all species →		DomainFYVE zinc fingerInterproscan
IPR017455
all species →		DomainZinc finger, FYVE-relatedInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR46275
all species →		HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0035091
all species →		Molecular Functionphosphatidylinositol bindingInterproscan
GO:0043130
all species →		Molecular Functionubiquitin bindingInterproscan
GO:0005769
all species →		Cellular Componentearly endosomeInterproscan
GO:0031623
all species →		Biological Processreceptor internalizationInterproscan
GO:0032456
all species →		Biological Processendocytic recyclingInterproscan
GO:0046872
all species →		Molecular Functionmetal ion 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
KOEnzymeEnzyme IDPathwayMap IDSource
K12182HGS, HRS, VPS27; hepatocyte growth factor-regulated tyrosine kinase substrate-Membrane traffickingko04131deepkoala

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_g07.12004_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
222.1Max TPM
115.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 110.27 181.59
Whole embryo · Triptolide 20 uM 4 4 153.47 222.08
Whole embryo · DMSO 0.5% 4 4 126.13 178.63

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 181.59
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 177.04
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 173.94
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 173.79
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 173.00
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 171.35
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 168.91
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 164.53
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 160.94
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 158.33
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 156.80
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 152.51
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 149.52
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 137.81
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 122.59
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 112.18
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 112.17
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 111.03
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 107.26
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 106.36
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 103.08
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 102.73
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 97.29
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 96.94
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 85.23
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 85.14
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 83.70
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 81.76
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 71.46
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 71.08
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 35.56
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 25.14
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 20.44
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 17.60
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 12.33
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 8.48
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 222.08
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 206.81
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 94.07
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 90.91
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 178.63
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 165.42
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 80.40
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 80.05

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 correlated25HSymV2.0_g05.09666_t10.974651726564235
Negatively correlated6HSymV2.0_g03.05943_t1-0.907213471571336

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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