hnf1ba HNF1 homeobox Ba [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hnf1baprovided by ZNC
Official Full Name: HNF1 homeobox Baprovided by ZNC
Primary source: ZFIN:ZDB-GENE-020104-1
See related: Ensembl:ENSDARG00000006615 AllianceGenome:ZFIN:ZDB-GENE-020104-1
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: mst; tcf2; hnf1b; vhnf1; chunp6877
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein dimerization activity. Involved in hindbrain development. Acts upstream of or within several processes, including embryonic organ development; hindbrain development; and liver development. Predicted to be active in nucleus. Is expressed in several structures, including digestive system; heart; neural plate; posterior neural keel; and pronephros. Human ortholog(s) of this gene implicated in kidney disease; pancreas disease; renal cell carcinoma; renal cysts and diabetes syndrome; and type 2 diabetes mellitus. Orthologous to human HNF1B (HNF1 homeobox B). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: chromosome: 15

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2025_04	current	GRCz12tu (GCF_049306965.1)	15	NC_133190.1 (18427733..18443547, complement)
RS_2024_08	previous assembly	GRCz11 (GCF_000002035.6)	15	NC_007126.7 (15997149..16012963, complement)

Chromosome 15 - NC_133190.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data show that hnf1ba generates a permissive domain for Wnt signaling activity in the foregut endoderm
Title: Specification of hepatopancreas progenitors in zebrafish by hnf1ba and wnt2bb.
essential for normal segmentation of nephrons during kidney organogenesis
Title: HNF1β is essential for nephron segmentation during nephrogenesis.
Knockdown of pk1a led to decreased expression of vhnf1, a homeodomain gene previously shown to be involved in biliary development and in kidney cyst formation; forced expression of vhnf1 mRNA led to rescue of the pk1a morphant phenotype
Title: Disruption of planar cell polarity activity leads to developmental biliary defects.
It was concluded that hnf1b(hi2169) is hypomorphic to hnf1b(hi1843) and that, while hnf1b is required for r5/r6 gene expression in the hindbrain, r5/r6 gene expression can be experimentally induced independently of hnf1b anterior to the hindbrain.
Title: hnf1b genes in zebrafish hindbrain development.
vHNF1 plays crucial role at the earliest steps of liver induction: the acquisition of endoderm competence and the hepatic specification.
Title: Crucial role of vHNF1 in vertebrate hepatic specification.
Data show that zebrafish mutants for Tcf2 fail to specify a single lumen in their gut tube and instead develop multiple lumens, and show that Tcf2 controls single lumen formation by regulating claudin15 and Na+/K+-ATPase expression.
Title: Genetic control of single lumen formation in the zebrafish gut.
investigated the signaling pathways that regulate vhnf1 expression during pancreas development
Title: Vhnf1 acts downstream of Bmp, Fgf, and RA signals to regulate endocrine beta cell development in zebrafish.
Zebrafish tcf2 gene, composed of 9 exons, was mapped to linkage group LG15.
Title: Two distinct teleost hepatocyte nuclear factor 1 genes, hnf1alpha/tcf1 and hnf1beta/tcf2, abundantly expressed in liver, pancreas, gut and kidney of zebrafish.
vhnf1 acts largely independently of val to repress the rhombomere 4 'hox code' posterior to the rhombomere 4-5 boundary
Title: vhnf1 integrates global RA patterning and local FGF signals to direct posterior hindbrain development in zebrafish.
Data show that vhnf1 functions in two ways to subdivide the zebrafish caudal hindbrain domain (r4-r7) into individual rhombomeres.
Title: vhnf1 and Fgf signals synergize to specify rhombomere identity in the zebrafish hindbrain.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

fd55e06.x1 (e-PCR)
- UniSTS:195664

fb77h02.y1 (e-PCR)
- UniSTS:191393

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein dimerization activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Process	Evidence Code	Pubs
involved_in animal organ development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in anterior/posterior pattern specification involved in pronephros development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification involved in pronephros development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within digestive tract morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic digestive tract development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endoderm formation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within glucose homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hepaticobiliary system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hindbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hindbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hindbrain morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within insulin secretion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within intrahepatic bile duct development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within liver development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within liver development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within liver development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within liver morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic placode formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic vesicle formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otolith development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within otolith morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pancreas development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within pancreas development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pancreas regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within rhombomere 5 development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhombomere 5 morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhombomere 6 development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhombomere 6 morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within semicircular canal morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within tube formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within type B pancreatic cell development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IC Inferred by Curator more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: hepatocyte nuclear factor 1-beta-A

Names: HNF-1-beta-A; HNF-1B-2; HNF-1B-A; HNF1 homeobox b; TCF-2; hepatocyte nuclear factor 1-beta; hepatocyte nuclear factor 1-beta-2; hob; transcription factor 2, hepatic; variant hepatic nuclear factor 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_131880.3 → NP_571955.3 hepatocyte nuclear factor 1-beta-A

See identical proteins and their annotated locations for NP_571955.3

Status: VALIDATED

Source sequence(s)

JBMGRA010000015

UniProtKB/Swiss-Prot

A1L1N5, Q6EEZ4, Q8UW01, Q90X59

UniProtKB/TrEMBL

A0A0R4IR44

Related

ENSDARP00000119593.1, ENSDART00000144138.3

Conserved Domains (3) summary

cd00086
Location:241 → 314

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam04812
Location:323 → 540

HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus

pfam04814
Location:12 → 180

HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus

RefSeqs of Annotated Genomes: GCF_049306965.1-RS_2025_04

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz12tu Primary Assembly

Genomic

NC_133190.1 Reference GRCz12tu Primary Assembly

Range

18427733..18443547 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021481477.3 → XP_021337152.1 hepatocyte nuclear factor 1-beta-A isoform X1

UniProtKB/Swiss-Prot

A1L1N5, Q6EEZ4, Q8UW01, Q90X59

UniProtKB/TrEMBL

A0A8M9Q0L2

Conserved Domains (3) summary

cd00086
Location:241 → 314

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam04812
Location:323 → 567

HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus

pfam04814
Location:12 → 180

HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
XM_073923308.1 → XP_073779409.1 hepatocyte nuclear factor 1-beta-A isoform X3
XM_021481478.3 → XP_021337153.1 hepatocyte nuclear factor 1-beta-A isoform X2

UniProtKB/TrEMBL

A0A8M9QC63

Conserved Domains (3) summary

cd00086
Location:111 → 184

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam04812
Location:193 → 437

HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus

pfam04814
Location:1 → 50

HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus