Detailed information of HSymV2.0_g12.21971_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_12:22004729...22013025
NR annotation: XP_047136050.1, eukaryotic translation initiation factor 4B [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
P23588Eukaryotic translation initiation factor 4B OS=Homo sapiens OX=9606 GN=EIF4B PE=1 SV=2
Q8BGD9Eukaryotic translation initiation factor 4B OS=Mus musculus OX=10090 GN=Eif4b PE=1 SV=1
O14369Probable RNA-binding protein sce3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=sce3 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004997 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00076
all species →		RRM_1RNA recognition motifDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000504
all species →		DomainRNA recognition motif domainInterproscan
IPR012677
all species →		Homologous_superfamilyNucleotide-binding alpha-beta plait domain superfamilyInterproscan
IPR035979
all species →		Homologous_superfamilyRNA-binding domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23236
all species →		EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4HInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0003676
all species →		Molecular Functionnucleic acid 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
K03258EIF4B; translation initiation factor 4B-Translation factorsko03012deepkoala

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_g12.21971_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
564.3Max TPM
276.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 271.11 564.34
Whole embryo · Triptolide 20 uM 4 4 284.78 425.92
Whole embryo · DMSO 0.5% 4 4 318.24 421.97

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 564.34
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 442.56
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 437.55
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 434.11
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 426.11
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 424.16
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 418.76
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 365.97
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 352.66
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 315.07
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 311.55
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 303.67
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 295.00
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 294.08
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 292.32
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 276.69
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 273.23
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 263.60
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 262.64
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 256.82
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 254.74
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 244.84
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 221.20
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 216.35
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 198.99
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 189.64
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 188.24
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 187.74
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 162.26
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 160.85
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 160.40
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 143.60
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 129.85
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 114.29
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 108.67
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 67.43
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 425.92
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 395.44
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 187.12
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 130.64
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 421.97
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 415.82
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 230.36
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 204.80

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 correlated36HSymV2.0_g09.16396_t10.952393011149812
Negatively correlated7HSymV2.0_g14.24473_t1-0.808290392084587

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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