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LOC107988042 MITF-A promoter region [ Homo sapiens (human) ]

Gene ID: 107988042, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107988042
Gene description
MITF-A promoter region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: promoter, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region represents the promoter of the A variant of the melanogenesis associated transcription factor gene. This sequence is activated by binding of paired box proteins and repressed by visual system homeobox 2. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC107988042 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (69737258..69739699)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (69774156..69776597)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (69786409..69788751)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FERM domain containing 4B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:69534465-69535137 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:69560923-69561519 Neighboring gene RNA binding motif protein 43 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:69655392-69655947 Neighboring gene H1-8 pseudogene 1 Neighboring gene NFE2L2 motif-containing MPRA enhancer 231 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:69818568-69819767 Neighboring gene RNA, 7SL, cytoplasmic 418, pseudogene Neighboring gene MITF-H promoter region Neighboring gene melanocyte inducing transcription factor Neighboring gene MITF-M distal enhancer Neighboring gene MITF-M promoter region Neighboring gene survival associated mitochondrial melanoma specific oncogenic non-coding RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20057 Neighboring gene RNA binding region (RNP1, RRM) containing 3 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Loss of MITF expression during human embryonic stem cell differentiation disrupts retinal pigment epithelium development and optic vesicle cell proliferation. Capowski EE, et al. Hum Mol Genet, 2014 Dec 1. PMID 25008112, Free PMC Article
  2. Structural organization of the human microphthalmia-associated transcription factor gene containing four alternative promoters. Udono T, et al. Biochim Biophys Acta, 2000 Apr 25. PMID 10760582
  3. Retinal pigmented epithelium determination requires the redundant activities of Pax2 and Pax6. Bäumer N, et al. Development, 2003 Jul. PMID 12756174
  4. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 14519
  • MITF promoter 1A

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.

Genomic

  1. NG_050804.2 

    Range
    101..2542
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    69737258..69739699
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    69774156..69776597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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