Detailed information of HSymV2.0_g09.15288_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_9:7005143...7006445
NR annotation: XP_012557843.2, lysM and putative peptidoglycan-binding domain-containing protein 2 [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
Q5PQ30LysM and putative peptidoglycan-binding domain-containing protein 1 OS=Xenopus laevis OX=8355 GN=lysmd1 PE=2 SV=1
Q6DEF4LysM and putative peptidoglycan-binding domain-containing protein 2 OS=Danio rerio OX=7955 GN=lysmd2 PE=2 SV=1
Q3B7I8LysM and putative peptidoglycan-binding domain-containing protein 2 OS=Xenopus tropicalis OX=8364 GN=lysmd2 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008244 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01476
all species →		LysMLysM domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR018392
all species →		DomainLysM domainInterproscan
IPR036779
all species →		Homologous_superfamilyLysM domain superfamilyInterproscan
IPR045030
all species →		FamilyLysM and putative peptidoglycan-binding domain-containing protein 1-4Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR20932
all species →		LYSM AND PUTATIVE PEPTIDOGLYCAN-BINDING DOMAIN-CONTAINING PROTEINInterproscan

 Gene Ontology
No Gene Ontology signature was recorded for HSymV2.0_g09.15288_t1 in Hydractinia symbiolongicarpus.
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_g09.15288_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_g09.15288_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
104.4Max TPM
64.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 69.36 104.45
Whole embryo · Triptolide 20 uM 4 4 48.28 57.34
Whole embryo · DMSO 0.5% 4 4 31.00 35.24

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 104.45
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 100.84
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 97.26
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 93.47
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 92.36
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 89.75
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 89.29
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 88.95
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 88.07
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 87.77
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 84.55
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 84.53
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 75.89
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 74.12
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 72.37
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 72.04
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 71.75
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 68.95
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 68.67
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 68.40
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 68.34
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 67.29
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 65.60
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 63.65
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 63.61
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 61.86
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 59.14
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 55.44
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 51.60
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 50.97
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 48.77
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 39.27
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 37.91
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 33.39
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 28.87
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 27.81
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 57.34
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 54.09
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 49.30
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 32.39
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 35.24
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 34.29
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 27.79
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 26.70

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_g06.11077_t10.896552408713246
Negatively correlated42HSymV2.0_g03.05847_t1-0.801429651976141

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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