Detailed information of HOLI00522.G16908 in Hydra oligactis

Genomic Location: HOLI00522:241652...242282
NR annotation: TXH94418.1, transcriptional regulator GcvA [Rheinheimera sp.]
Species Hydra oligactis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P0A9F8Glycine cleavage system transcriptional activator OS=Escherichia coli O157:H7 OX=83334 GN=gcvA PE=3 SV=1
P0A9F7Glycine cleavage system transcriptional activator OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) OX=199310 GN=gcvA PE=3 SV=1
P0A9F6Glycine cleavage system transcriptional activator OS=Escherichia coli (strain K12) OX=83333 GN=gcvA PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0014281 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03466
all species →		LysR_substrateLysR substrate binding domainFamilyInterproscan
PF00126
all species →		HTH_1Bacterial regulatory helix-turn-helix protein, lysR familyDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000847
all species →		DomainTranscription regulator HTH, LysRInterproscan
IPR005119
all species →		DomainLysR, substrate-bindingInterproscan
IPR036388
all species →		Homologous_superfamilyWinged helix-like DNA-binding domain superfamilyInterproscan
IPR036390
all species →		Homologous_superfamilyWinged helix DNA-binding domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR30537
all species →		HTH-TYPE TRANSCRIPTIONAL REGULATORInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003700
all species →		Molecular FunctionDNA-binding transcription factor activityInterproscan
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0006351
all species →		Biological ProcessDNA-templated transcriptionInterproscan
GO:0043565
all species →		Molecular Functionsequence-specific DNA 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 HOLI00522.G16908.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Hydra oligactis 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Hydra oligactis, 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.no expression matrix–
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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