Detailed information of HSymV2.0_g09.16540_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_9:14354159...14367658
NR annotation: XP_047133185.1, protrudin isoform X1 [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
Q5ZL36Protrudin OS=Gallus gallus OX=9031 GN=ZFYVE27 PE=2 SV=1
Q6P7B7Protrudin OS=Rattus norvegicus OX=10116 GN=Zfyve27 PE=1 SV=2
Q5T4F4Protrudin OS=Homo sapiens OX=9606 GN=ZFYVE27 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005149 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00076
all species →		RRM_1RNA recognition motifDomainInterproscan
PF01363
all species →		FYVEFYVE zinc fingerDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000504
all species →		DomainRNA recognition motif domainInterproscan
IPR017455
all species →		DomainZinc finger, FYVE-relatedInterproscan
IPR000306
all species →		DomainFYVE zinc fingerInterproscan
IPR035979
all species →		Homologous_superfamilyRNA-binding domain superfamilyInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR042405
all species →		FamilyProtrudinInterproscan
IPR012677
all species →		Homologous_superfamilyNucleotide-binding alpha-beta plait domain superfamilyInterproscan
IPR011011
all species →		Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14543
all species →		PROTRUDINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0046872
all species →		Molecular Functionmetal ion bindingInterproscan
GO:0003676
all species →		Molecular Functionnucleic acid bindingInterproscan
GO:0016192
all species →		Biological Processvesicle-mediated transportInterproscan
GO:0043621
all species →		Molecular Functionobsolete protein self-associationInterproscan
GO:0071782
all species →		Cellular Componentendoplasmic reticulum tubular networkInterproscan
GO:0071787
all species →		Biological Processendoplasmic reticulum tubular network formationInterproscan
GO:0072659
all species →		Biological Processprotein localization to plasma membraneInterproscan

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_g09.16540_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_g09.16540_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
1,146.9Max TPM
422.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 434.71 1,146.91
Whole embryo · Triptolide 20 uM 4 4 365.52 469.57
Whole embryo · DMSO 0.5% 4 4 369.88 442.68

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 1,146.91
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 880.69
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 618.45
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 610.53
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 585.44
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 565.92
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 540.56
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 539.08
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 515.30
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 514.59
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 505.73
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 499.42
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 445.84
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 444.53
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 424.45
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 419.90
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 410.85
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 394.51
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 393.84
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 389.94
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 384.41
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 368.64
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 366.63
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 361.81
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 352.68
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 340.48
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 332.19
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 323.83
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 287.40
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 272.42
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 249.79
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 248.84
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 248.72
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 240.09
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 231.44
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 193.69
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 469.57
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 427.86
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 295.82
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 268.83
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 442.68
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 430.75
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 303.73
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 302.34

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 correlated18HSymV2.0_g07.11640_t10.936136604082314
Negatively correlated11HSymV2.0_g13.23044_t1-0.810071651960677

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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