Detailed information of HOLI00691.G35026 in Hydra oligactis

Genomic Location: HOLI00691:135436...136842
NR annotation: TXH90363.1, MAG: Y-family DNA polymerase [Rhodoferax 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
P04152Protein UmuC OS=Escherichia coli (strain K12) OX=83333 GN=umuC PE=1 SV=2
P22494Protein UmuC OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=umuC PE=3 SV=1
P18642Protein ImpB OS=Salmonella typhimurium OX=90371 GN=impB PE=3 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13438
all species →		DUF4113Domain of unknown function (DUF4113)DomainInterproscan
PF11799
all species →		IMS_CimpB/mucB/samB family C-terminal domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR043502
all species →		Homologous_superfamilyDNA/RNA polymerase superfamilyInterproscan
IPR025188
all species →		DomainDomain of unknown function DUF4113Interproscan
IPR050116
all species →		FamilyDNA polymerase type-YInterproscan
IPR001126
all species →		DomainUmuC domainInterproscan
IPR017961
all species →		DomainDNA polymerase, Y-family, little finger domainInterproscan
IPR043128
all species →		Homologous_superfamilyReverse transcriptase/Diguanylate cyclase domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11076
all species →		DNA REPAIR POLYMERASE UMUC / TRANSFERASE FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003887
all species →		Molecular FunctionDNA-directed DNA polymerase activityInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0009432
all species →		Biological ProcessSOS responseInterproscan
GO:0042276
all species →		Biological Processerror-prone translesion synthesisInterproscan
GO:0006281
all species →		Biological ProcessDNA repairInterproscan
GO:0003684
all species →		Molecular Functiondamaged 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 HOLI00691.G35026.

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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