Detailed information of FUN_018714-T2 in Dendrogyra cylindrus

Genomic Location: contig_33:3340755...3376949
NR annotation: XP_020624574.1, hepatocyte nuclear factor 4-gamma-like isoform X4 [Orbicella faveolata]
Species Dendrogyra cylindrus · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9WUU6Hepatocyte nuclear factor 4-gamma OS=Mus musculus OX=10090 GN=Hnf4g PE=2 SV=2
Q14541Hepatocyte nuclear factor 4-gamma OS=Homo sapiens OX=9606 GN=HNF4G PE=1 SV=3
P49698Hepatocyte nuclear factor 4-alpha OS=Mus musculus OX=10090 GN=Hnf4a PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000188 (this species only) · gene tree & orthology
Transcription factor familyMiscellaneous · all TF in this species
Transcription factor familyNGFIB-like · all TF in this species
Transcription factor familySF-like · all TF in this species
Transcription factor familyTHR-like · all TF in this species
Transcription factor familyGCNF-like · all TF in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00105
all species →		zf-C4Zinc finger, C4 type (two domains)DomainInterproscan
PF00104
all species →		Hormone_recepLigand-binding domain of nuclear hormone receptorDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR035500
all species →		Homologous_superfamilyNuclear hormone receptor-like domain superfamilyInterproscan
IPR049636
all species →		DomainHepatocyte nuclear factor 4-like, DNA-binding domainInterproscan
IPR013088
all species →		Homologous_superfamilyZinc finger, NHR/GATA-typeInterproscan
IPR000536
all species →		DomainNuclear hormone receptor, ligand-binding domainInterproscan
IPR001628
all species →		DomainZinc finger, nuclear hormone receptor-typeInterproscan
IPR001723
all species →		FamilyNuclear hormone receptorInterproscan
IPR000003
all species →		FamilyRetinoid X receptor/HNF4Interproscan
IPR049635
all species →		DomainHepatocyte nuclear factor 4, ligand-binding domainInterproscan
IPR050274
all species →		FamilyNuclear hormone receptor family NR2 subfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR24083
all species →		NUCLEAR HORMONE RECEPTORInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000978
all species →		Molecular FunctionRNA polymerase II cis-regulatory region sequence-specific DNA bindingInterproscan
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0008270
all species →		Molecular Functionzinc ion bindingInterproscan
GO:0003700
all species →		Molecular FunctionDNA-binding transcription factor activityInterproscan
GO:0043565
all species →		Molecular Functionsequence-specific DNA bindingInterproscan
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0003707
all species →		Molecular Functionnuclear steroid receptor activityInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0004879
all species →		Molecular Functionnuclear receptor activityInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan
GO:0030154
all species →		Biological Processcell differentiationInterproscan
GO:0048856
all species →		Biological Processanatomical structure developmentInterproscan

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
K07292NR2A1, HNF4A; hepatocyte nuclear factor 4-alpha-Nuclear receptorsko03310deepkoala

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 Dendrogyra cylindrus 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 Dendrogyra cylindrus, 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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