hmx3a H6 family homeobox 3a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hmx3aprovided by ZNC
Official Full Name: H6 family homeobox 3aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-001020-1
See related: Ensembl:ENSDARG00000070955 AllianceGenome:ZFIN:ZDB-GENE-001020-1
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: hmx3; Nkx5-1; nkx5.1; zgc:109845
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within inner ear morphogenesis and posterior lateral line development. Predicted to be active in nucleus. Is expressed in dorsolateral placode; nervous system; neural rod; neural tube; and otic vesicle. Orthologous to human HMX3 (H6 family homeobox 3). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 17

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	17	NC_007128.7 (21790606..21793050, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (21770770..21773274, complement)

Chromosome 17 - NC_007128.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hmx3a Has Essential Functions in Zebrafish Spinal Cord, Ear and Lateral Line Development.
Title: Hmx3a Has Essential Functions in Zebrafish Spinal Cord, Ear and Lateral Line Development.
hmx3 acts as cell autonomous factors required redundantly for cell fate specification and differentiation during inner ear and lateral line development
Title: Pivotal role of hmx2 and hmx3 in zebrafish inner ear and lateral line development.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inner ear morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within otolith development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within posterior lateral line development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within posterior lateral line neuromast primordium migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within 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 spinal cord 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	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein HMX3

Names: H6 family homeobox 3; homeo box (H6 family) 3; homeobox protein H6 family member 3; homeobox protein Nkx-5.1

NCBI Reference Sequences (RefSeq)

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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_131634.2 → NP_571709.2 homeobox protein HMX3

Status: VALIDATED

Source sequence(s)

AL773596, EH585322

UniProtKB/Swiss-Prot

A9Y2A8, Q504H8, Q9DFB1

UniProtKB/TrEMBL

A0A8N7UZL9, F1QMB1

Related

ENSDARP00000095383.4, ENSDART00000104612.5

Conserved Domains (1) summary

pfam00046
Location:173 → 226

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007128.7 Reference GRCz11 Primary Assembly

Range

21790606..21793050 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005158695.5 → XP_005158752.1 homeobox protein HMX3 isoform X1

UniProtKB/Swiss-Prot

A9Y2A8, Q504H8, Q9DFB1

UniProtKB/TrEMBL

A0A8M2B544

Conserved Domains (1) summary

pfam00046
Location:172 → 225

Homeobox; Homeobox domain