Gene detail

Detailed information of amic_s0041.g48.t1 in Acropora microphthalma

Genomic Location: sc0000041_pilon:735787...744932
NR annotation: XP_015779439.1, PREDICTED: hepatocyte nuclear factor 1-beta-A-like isoform X1 [Acropora digitifera]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

amic_s0041.g48.t1

CGTAACGAACGGCTCCGTGCTGTTGCGCTGACCTATAATGAATGCATGCTCAAAATGGAGTCGTACGCTGTAGCGCCAGTGACTGTAACACAGGCCTCGCAAACTATGCAGCATCGTAATGGCTGATGAGCTCACTGACCTTCAAAAGCAGTTGCTCGGTGCGTTAGTTGAGAGCGGTATCACCAAAGATGCACTCCTCAATTCCCTGGACGCTCTTTTTGCCAAGCAGGTTCCAGGCATTACAGAAAGCTTAGCCAGCAGCCCGGCTACTGATTCCGAACAAGAAATCAAACCAACCGATTACAACGATGATCCGCCGCCGCAATGTATAGTGAGCAATAGCGGCACCGTTAAAATTGAAGAAGCGTCCAAACGCGTTGTGATGCAAGACGCGCGCTTGGAAGTAGACCGAGAAATGAATTTTCTTGAACATATGCTAAGAATGGATCCTTGGCAAGCTGCCAAGATAATTAAAATGTACATGCAGCAGCATAACATCCCACAACGAGAGGTAGTGGAGTCCACTGGACTGAATCAGAGTCACCTGTCACAGCACCTCAACAAGGGAACACCAATGAAAACTAACAAAAGAGCTGCACTTTACACTTGGTTTGAAAACAAGAGGAAAGAAATCATAGAACAATACAATTCACCCAGGAAGAGGCTTATTTCAGAAACAGAAAATACTGGGGAGATCCCAACCAAAAAGACCAGAAGAAATCGCTTTAAATGGGGACCTGCATCTACAAACTTACTGTACCATTCCTACGAAGAGCAAAAAAATCCCTCTAAGGAAGAAAGAGAAGCACTAGTTGAGGCTTGTAATAGAGCTGAGTGCAACCAGAGGGGTGTTCCCTATGGCAATGTAGAGGGGCTTGGTCCGAACCTTGTGACTGAGAGCCGAGTGTACAACTGGTTTGCCAACAGACGGAAAGAGGAAACATTCAGATTGAAGCTGGCAATTGATGCAGCAAGCTATCCTGATGCTTCTGTTTCTTTTCAAGGACAAGGAGTTGTTACACAGACATTAGAGAGTGCAGCTTTGCCAACTGTGATGTCACCAGTTGTTTCTCCTACCACACTCACTGCCTCAATGCCATCTATGAACAAGAGCTCATTACAACAAACAATGCCTCTAGATCCAATTACAACCCAACAAACACAGCAACTACGGTTGAATACAGCCCATGTCAATCACAGTGCTCAAATGGCCGCCGGGCAGCAAGGCCAACCGCAACCCAGTCAACATCAGGGAGTTCCATCTATGATGAGTAGCTTCGTCCCTACTGCAGTTCCCCAACAGTTGCCACTGAGCATGGCAATGATGCCTCCTTCAGGGATTCCAGCTACTTGTGCCACTGTTCAACCACAAGTGATGCAGACGTCAAGTGTGAGCCATCAACAACATACAGTGGTACCAGGCATTGGTCAAATCCCGGTCATTGTATCAATGCCTGGTGGTATGGATGGATTGCCTCAAGGCATGCCACAGTTACCAGAAAGCCTCGCACAAATGGCAACAGCAACCCATTTAGTCCACATGCATCCTGTTACTGTGACAACACTTCCAATGGCACCAAGTTTGCAGCCAGTCTCATGCAGTGAAGTATCATTGCCTCCAGCTCTTCAACCCATACCTGTGATGTCATCAATGGTGCAGATACCATCAGCCCAAGGATCCCTCCCTGTCCCTGTTGCAGCAATCAATATTCCCAGGGATGGACCTCAATCCCCAATTTATGAAGTGAAACTTGAGGCAGCAGTCAAGGATGTGGCAATAGAGAAAGCTGGACCTTTTATCAACGCACCCAAGGGAGGAATGAAAGTCAAATGTGAAGGAGTCAAAGTGGAAAATGGTGAGGAAGCAATAATTGTCTCATCATCACCAACTGTTCCTGTGGCGGAAAATGTGATAGTAACAACTCAAGGTGGAGAACTGAGACATGAAGAAAGGCAAGCATGTGAAAAGGATAAAACAGACATTTTTATCTCTGAAAGTACTCAGTTACATTCTGTTGAGGGCATGCCAGGAAGATGATGCTGATAATTTTATGTATGTCACAAAAATAATATCTTAGTCGTTTACTAGCAGGCAGACTGAGTCAATTTAGGGAGAGGGCCTTAAAACATTTCAAGAACAGGAAAGATTTGCTGCACTTTGATACTTTTAATAGTAAAGTAACTATCTTGTTATAGTACCAATTGTACTCTACAATTACCATACTTTTAATTATTGAAAGGTGCATGGGTAATTCAAAGATGGTTTGCAAGGAATTATGTGCCTCCAAGAAGGCTGAAGGTGAGCAAAATAGCTCGCTACTTTGTAAATATTCTGTAAGGCCTGGGAGCTTGAACATTAGGCATTTATTGAGTCATGGACAGCAACCAAAAGCGTGAAATTCATATTTTTAGGAGCAGTGACTTTGTCTAGCTTTGAATGAATTGTCTCTGGCAGAGCAGAGTAATTAATacatgaaaaagatgaaaaacttgaaaaacatagaaaaacTTGTGCTTGAATTCCCCATTAAGAAGTTGTGTGCTTTGCAGTATTCACTCAAATAACAATTCTATATAGCCCTCCGCTGATGAAAGTGGTGGGTTTGGTTGTGGTAATATCTAAATCAAATAAAATTATTATTTTCATAAACTTAATTAGTATTAAGTGACTGTCAGATCGGTAAGCATCATTCTGTTTCTGTGGCTGGTTCACAGTAATGTGAAGGCTCCATCTTGTCAAAAAAATATTCTTTTAGGTTGTCGCGTAAGGAAAGGAAGTGATTGATTGGTGTGTCCAGGAGGGAAAAAATATTAATTTATAATCCAATGCATGCATGGAATGCACTCAGATTTAAATGGCTAGGGCACAACCAATTAAAGGCATAATTCAGTAGTTAAAATTATTTGTGTGACAACTCACCAAACAACTGTCAATTACTGATTGATTTGAATCTAGAGGTCATGTTAAATTTGTGAAAGTGAGTGCAGTGCTTGGAAGGACTTTCTTACAACACATTTTTGACAATAGTGGATTGACTATGGATGTGGGATTCTTTTCTTCTTTGAAGTTACTGGTGAACCTGTGGCACAAGTAAACTATTGCATTTGGATCATTGACTTGTTGTGAATTAGTCTTGTTTTATTTGAAGGGAGTAATAATTTACACACAATCAATTGTTTTTTTGCACCATTATGCTTGCAATAAAACCAACCTGTTAGTTTCATAGCAAAAGTTCTTGTCGCAAATAACACTTGCCCAAAAACATTGCAAAGCAGTTGTGCCCTCCGCCAGTCAATAAAACCGCAATCTATCTTTATTTAGTTTTATCTTATTGTCAGATTTGTTCCGTTTGACTTATTTTTACAATATTATTGTAAATAGTGGAATGCTTTGCGAGAAAGCCAAGTGTCATAACCAGATATCTATTATTTTAAAAAATGAATGTCTTGTAATTAGAGAAGAATGGAACTGGAGTCAGATTATTTATGGTTATTTTCATCACTTTGTGAGAATTTAAAAAATACATAATTTATTCAATCTTTTATCCATTGATGAGCATTAAGTATTTTTTTAAAAAAACAGTTATGTTGCATATGTCTACCAACAAATTATCGAAATTATTGCTAAATAAAGGTCCCTGATTTAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P27889	Hepatocyte nuclear factor 1-beta OS=Mus musculus OX=10090 GN=Hnf1b PE=1 SV=2
P35680	Hepatocyte nuclear factor 1-beta OS=Homo sapiens OX=9606 GN=HNF1B PE=1 SV=1
Q5RER5	Hepatocyte nuclear factor 1-beta OS=Pongo abelii OX=9601 GN=HNF1B PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008925 (this species only) · gene tree & orthology
Transcription factor family	Homeobox · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04814 all species →	HNF-1_N	Hepatocyte nuclear factor 1 (HNF-1), N terminus	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR023219 all species →	Homologous_superfamily	Hepatocyte nuclear factor 1, N-terminal domain superfamily	Interproscan
IPR006899 all species →	Domain	Hepatocyte nuclear factor 1, N-terminal	Interproscan
IPR044869 all species →	Domain	HNF-1, POU-specific (POUs) atypical domain	Interproscan
IPR010982 all species →	Homologous_superfamily	Lambda repressor-like, DNA-binding domain superfamily	Interproscan
IPR039066 all species →	Family	Hepatocyte nuclear factor 1	Interproscan
IPR044866 all species →	Domain	HNF-1, dimerization domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11568 all species →	HEPATOCYTE NUCLEAR FACTOR 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0045893 all species →	Biological Process	positive regulation of DNA-templated transcription	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0001889 all species →	Biological Process	liver development	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0030073 all species →	Biological Process	insulin secretion	Interproscan
GO:0031016 all species →	Biological Process	pancreas development	Interproscan

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 amic_s0041.g48.t1.

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 Acropora microphthalma 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 Acropora microphthalma, 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.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search 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 found	open →
Expression heatmap	Draw 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 / orthogroup	Look 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 analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →