mitfa melanocyte inducing transcription factor a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: mitfaprovided by ZNC
Official Full Name: melanocyte inducing transcription factor aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990910-11
See related: Ensembl:ENSDARG00000003732 AllianceGenome:ZFIN:ZDB-GENE-990910-11
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: nacre; z3A.1
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific. Acts upstream of or within with a positive effect on melanocyte differentiation. Acts upstream of or within circadian rhythm; pigmentation; and transcription, DNA-templated. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including immature eye; iridoblast; melanoblast; neural crest; and pigment cell. Human ortholog(s) of this gene implicated in Tietz syndrome; Tietze's syndrome; Waardenburg syndrome type 2A; Waardenburg's syndrome; and familial melanoma. Orthologous to human MITF (melanocyte inducing transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 6

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	6	NC_007117.7 (43399763..43433295)
105	previous assembly	GRCz10 (GCF_000002035.5)	6	NC_007117.6 (43396040..43435759)

Chromosome 6 - NC_007117.7 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?

mitfa deficiency promotes immune vigor and potentiates antitumor effects in zebrafish.
Title: mitfa deficiency promotes immune vigor and potentiates antitumor effects in zebrafish.
pH-controlled histone acetylation amplifies melanocyte differentiation downstream of MITF.
Title: pH-controlled histone acetylation amplifies melanocyte differentiation downstream of MITF.
Mitf-family transcription factor function is required within cranial neural crest cells to promote choroid fissure closure.
Title: Mitf-family transcription factor function is required within cranial neural crest cells to promote choroid fissure closure.
Melanosome maturation proteins Oca2, Mitfa and Vps11 are differentially required for cisplatin resistance in zebrafish melanocytes.
Title: Melanosome maturation proteins Oca2, Mitfa and Vps11 are differentially required for cisplatin resistance in zebrafish melanocytes.
Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution.
Title: Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution.
This shift occurs as pigment cells arise from the neural crest and depends on mitfa, an ortholog of MITF, a key regulator of melanocyte development that is also targeted by oncogenic BMP signaling.
Title: Regulation of zebrafish melanocyte development by ligand-dependent BMP signaling.
Zebrafish gene was identified that when mutated produces semi-viable offspring and that may serve as a model of human diseases that have both pigmentation and neurological symptoms.
Title: Touchtone promotes survival of embryonic melanophores in zebrafish.
Genetic interaction between tfap2a and mitfa suggest that the factors encoded by these genes regulate shared targets in melanocytes, possibly within single or converging pathways.
Title: TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF.
we report an efficient transgenic method of utilizing pigmentation rescue of nacre mutant fish for accurate naked-eye identification of both mosaic founders and stable transgenic zebrafish
Title: Efficient transgenesis mediated by pigmentation rescue in zebrafish.
This work explains the temperature sensitivity of the mitfavc7 mutation to be due to an unusual intron 6 mutation that leads to reduced levels of wild-type mitfa RNA.
Title: Temperature-sensitive splicing of mitfa by an intron mutation in zebrafish.

Submit: New GeneRIF Correction See all GeneRIFs (17)

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
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	IDA Inferred from Direct Assay 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	IEA Inferred from Electronic Annotation more info
enables protein dimerization activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-templated transcription	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within cellular response to tumor cell	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within circadian rhythm	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within closure of optic fissure	IGI Inferred from Genetic Interaction more info	PubMed
involved_in melanocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within melanocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within_positive_effect melanocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within melanocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_positive_effect melanocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pigmentation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pigmentation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of melanocyte differentiation	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 regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info

Component	Evidence Code	Pubs
located_in nucleoplasm	IC Inferred by Curator more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: melanocyte inducing transcription factor a; microphthalmia-associated transcription factor

Names: Mitf-related; Mitf2; microphthalmia-associated transcription factor a; microphthalmia-related protein; nac

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_001362262.1 → NP_001349191.1 melanocyte inducing transcription factor a isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

BX927362

Conserved Domains (4) summary

cd00083
Location:134 → 194

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam09332
Location:73 → 225

Mcm10; Mcm10 replication factor

pfam11851
Location:222 → 329

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:1 → 29

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
NM_130923.2 → NP_570998.1 melanocyte inducing transcription factor a isoform 1

See identical proteins and their annotated locations for NP_570998.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

BX927362

UniProtKB/TrEMBL

F6P160, Q789G8, Q9PWC2

Related

ENSDARP00000056456.4, ENSDART00000056457.5

Conserved Domains (3) summary

cd00083
Location:197 → 257

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam11851
Location:285 → 392

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:11 → 90

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

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_007117.7 Reference GRCz11 Primary Assembly

Range

43399763..43433295

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021476775.1 → XP_021332450.1 microphthalmia-associated transcription factor isoform X2

UniProtKB/TrEMBL

A0A8M9QF67

Related

ENSDARP00000114096.2, ENSDART00000143374.4

Conserved Domains (4) summary

cd00083
Location:136 → 196

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam09332
Location:73 → 227

Mcm10; Mcm10 replication factor

pfam11851
Location:224 → 331

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:1 → 29

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_021476774.1 → XP_021332449.1 microphthalmia-associated transcription factor isoform X1

UniProtKB/TrEMBL

A0A8M9Q5Y7

Conserved Domains (4) summary

cd00083
Location:196 → 256

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam09332
Location:134 → 287

Mcm10; Mcm10 replication factor

pfam11851
Location:284 → 391

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:11 → 90

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus