Detailed information of HSymV2.0_g14.24895_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_14:19533020...19548831
NR annotation: XP_047123371.1, protein SEC13 homolog [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
Q3ZCC9Protein SEC13 homolog OS=Bos taurus OX=9913 GN=SEC13 PE=2 SV=1
P55735Protein SEC13 homolog OS=Homo sapiens OX=9606 GN=SEC13 PE=1 SV=3
Q9D1M0Protein SEC13 homolog OS=Mus musculus OX=10090 GN=Sec13 PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004440 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00400
all species →		WD40WD domain, G-beta repeatRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR015943
all species →		Homologous_superfamilyWD40/YVTN repeat-like-containing domain superfamilyInterproscan
IPR001680
all species →		RepeatWD40 repeatInterproscan
IPR037363
all species →		FamilySec13/Seh1 familyInterproscan
IPR036322
all species →		Homologous_superfamilyWD40-repeat-containing domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11024
all species →		NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0005198
all species →		Molecular Functionstructural molecule activityInterproscan
GO:0006606
all species →		Biological Processprotein import into nucleusInterproscan
GO:0030127
all species →		Cellular ComponentCOPII vesicle coatInterproscan
GO:0031080
all species →		Cellular Componentnuclear pore outer ringInterproscan
GO:0032008
all species →		Biological Processpositive regulation of TOR signalingInterproscan
GO:0032527
all species →		Biological Processprotein exit from endoplasmic reticulumInterproscan
GO:0090114
all species →		Biological ProcessCOPII-coated vesicle buddingInterproscan

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
K14004SEC13; protein transport protein SEC13-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_g14.24895_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
375.9Max TPM
218.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 210.11 375.86
Whole embryo · Triptolide 20 uM 4 4 270.66 362.68
Whole embryo · DMSO 0.5% 4 4 246.37 313.33

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 375.86
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 356.75
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 300.67
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 299.98
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 285.35
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 270.71
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 269.60
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 261.60
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 259.18
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 252.46
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 241.17
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 234.74
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 232.55
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 232.38
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 228.48
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 223.17
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 218.22
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 183.98
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 182.56
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 181.34
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 180.56
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 180.41
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 179.64
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 175.44
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 171.80
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 163.25
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 157.78
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 150.73
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 147.47
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 147.20
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 145.77
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 145.47
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 144.93
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 136.74
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 129.52
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 116.39
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 362.68
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 339.39
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 201.35
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 179.22
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 313.33
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 307.79
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 182.91
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 181.46

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 correlated28HSymV2.0_g02.04297_t10.943735741329541
Negatively correlated6HSymV2.0_g13.22446_t1-0.77534246720357

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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