Detailed information of ENSSJYP00000016613.1 in Catostylus mosaicus

Genomic Location: chr4:2063561...2069689
NR annotation: XP_002160159.3, zinc finger protein ubi-d4 B isoform X2 [Hydra vulgaris]
Species Catostylus mosaicus · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q61103Zinc finger protein ubi-d4 OS=Mus musculus OX=10090 GN=Dpf2 PE=1 SV=1
Q92785Zinc finger protein ubi-d4 OS=Homo sapiens OX=9606 GN=DPF2 PE=1 SV=2
P58268Zinc finger protein ubi-d4 OS=Gallus gallus OX=9031 GN=REQ PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006254 (this species only) · gene tree & orthology
Ubiquitin familyE3|E3 activity RING|PHD · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF14051
all species →
DPF1-3_NDPF1-3, N-terminalFamilyInterproscan
PF00628
all species →
PHDPHD-fingerDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR019787
all species →
DomainZinc finger, PHD-fingerInterproscan
IPR013087
all species →
DomainZinc finger C2H2-typeInterproscan
IPR013083
all species →
Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR001965
all species →
DomainZinc finger, PHD-typeInterproscan
IPR011011
all species →
Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR025750
all species →
DomainDPF1-3, N-terminal domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45888
all species →
HL01030P-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003713
all species →
Molecular Functiontranscription coactivator activityInterproscan
GO:0042393
all species →
Molecular Functionhistone bindingInterproscan
GO:0042800
all species →
Molecular Functionhistone H3K4 methyltransferase activityInterproscan
GO:0044666
all species →
Cellular ComponentMLL3/4 complexInterproscan
GO:0045944
all species →
Biological Processpositive regulation of transcription by RNA polymerase IIInterproscan

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
K13196DPF2, REQ; zinc finger protein ubi-d4-Chromosome and associated proteinsko03036deepkoala

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 Catostylus mosaicus 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 Catostylus mosaicus, 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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