Detailed information of HSymV2.0_g14.24787_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_14:18026230...18033491
NR annotation: XP_002156849.1, LIM and SH3 domain protein 1 [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
O77506LIM and SH3 domain protein 1 OS=Oryctolagus cuniculus OX=9986 GN=LASP1 PE=1 SV=1
Q3B7M5LIM and SH3 domain protein 1 OS=Bos taurus OX=9913 GN=LASP1 PE=2 SV=1
Q5R5W0LIM and SH3 domain protein 1 OS=Pongo abelii OX=9601 GN=LASP1 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004325 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00880
all species →		NebulinNebulin repeatRepeatInterproscan
PF14604
all species →		SH3_9Variant SH3 domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000900
all species →		RepeatNebulin repeatInterproscan
IPR001452
all species →		DomainSH3 domainInterproscan
IPR036028
all species →		Homologous_superfamilySH3-like domain superfamilyInterproscan
IPR051759
all species →		FamilyLIM and SH3 domain-containing proteinInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR46218
all species →		LASPInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0005925
all species →		Cellular Componentfocal adhesionInterproscan
GO:0051015
all species →		Molecular Functionactin filament 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_g14.24787_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_g14.24787_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
398.3Max TPM
245.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 270.90 398.27
Whole embryo · Triptolide 20 uM 4 4 130.22 161.24
Whole embryo · DMSO 0.5% 4 4 127.84 133.85

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 398.27
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 383.36
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 372.89
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 363.92
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 357.06
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 354.81
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 352.29
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 343.73
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 342.00
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 319.46
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 316.62
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 302.36
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 293.47
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 289.21
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 288.96
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 285.69
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 279.21
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 279.03
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 277.95
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 275.21
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 272.80
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 262.67
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 252.32
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 237.46
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 236.06
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 226.53
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 225.05
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 216.52
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 216.42
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 212.55
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 198.89
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 158.69
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 144.83
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 141.02
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 140.11
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 134.83
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 161.24
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 156.32
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 109.34
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 93.98
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 133.85
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 130.78
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 125.86
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 120.87

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 correlated23HSymV2.0_g12.20860_t10.877032222881489
Negatively correlated74HSymV2.0_g04.06678_t1-0.878367565696391

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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