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msx1a muscle segment homeobox 1a [ Danio rerio (zebrafish) ]

Gene ID: 30527, updated on 27-Mar-2024


Official Symbol
msx1aprovided by ZNC
Official Full Name
muscle segment homeobox 1aprovided by ZNC
Primary source
See related
Ensembl:ENSDARG00000116118 AllianceGenome:ZFIN:ZDB-GENE-980526-312
Gene type
protein coding
RefSeq status
Danio rerio
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
mshE; msx1; msxe; cb435; msh-E; id:ibd5099; zgc:111928
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 otic placode formation. Predicted to be active in nucleus. Is expressed in several structures, including immature eye; nervous system; neural keel; pharyngeal arch; and regenerating fin. Human ortholog(s) of this gene implicated in cleft lip; cleft palate; orofacial cleft 5; tooth and nail syndrome; and tooth disease (multiple). Orthologous to human MSX1 (msh homeobox 1). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

See msx1a in Genome Data Viewer
chromosome: 14
Exon count:
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 14 NC_007125.7 (10906..12794, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 14 NC_007125.6 (241572..243460)

Chromosome 14 - NC_007125.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC110440195 Neighboring gene cytokine like 1 Neighboring gene syntaxin 18 Neighboring gene zinc finger and BTB domain containing 49 Neighboring gene Ly1 antibody reactive homolog (mouse)

Genomic regions, transcripts, and products


  • 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

Pathways from PubChem

General gene information


Clone Names

  • MGC111928

Gene Ontology Provided by ZFIN

Process Evidence Code Pubs
involved_in embryonic morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
acts_upstream_of_or_within otic placode formation IGI
Inferred from Genetic Interaction
more info
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
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

Preferred Names
homeobox protein MSX-1a
muscle segment homeobox E

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)

  1. NM_131273.1NP_571348.1  homeobox protein MSX-1a

    See identical proteins and their annotated locations for NP_571348.1


    Source sequence(s)
    ENSDARP00000147264.1, ENSDART00000188819.1
    Conserved Domains (1) summary
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly


  1. NC_007125.7 Reference GRCz11 Primary Assembly

    10906..12794 complement
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001033589.1: Suppressed sequence

    NM_001033589.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript or the N-terminus of the encoded protein.