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

Summary

Official Symbol: msx1aprovided by ZNC
Official Full Name: muscle segment homeobox 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-312
See related: Ensembl:ENSDARG00000116118 AllianceGenome:ZFIN:ZDB-GENE-980526-312
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: 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
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 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]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 14

Exon count:: 2

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_007125.7 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
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?

Data suggest that mutual antagonism between MsxB, C, and E and Distal-less proteins achieves a balance of function required for normal preplacodal differentiation and placement of the neural-nonneural border.
Title: Zebrafish msxB, msxC and msxE function together to refine the neural-nonneural border and regulate cranial placodes and neural crest development.

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General gene information

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Markers

fd07b11.x1 (e-PCR)
- UniSTS:204073

msxe (e-PCR), detects polymorphism
- UniSTS:186995

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

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	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

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 MSX-1a

Names: 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)

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

See identical proteins and their annotated locations for NP_571348.1

Status: PROVISIONAL

Source sequence(s)

U50563

UniProtKB/TrEMBL

Q90455

Related

ENSDARP00000147264.1, ENSDART00000188819.1

Conserved Domains (1) summary

pfam00046
Location:114 → 167

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007125.7 Reference GRCz11 Primary Assembly

Range

10906..12794 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001033589.1: Suppressed sequence

Description

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.