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LOC111811965 NF1 (neurofibromin 1) promoter region [ Homo sapiens (human) ]

Gene ID: 111811965, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111811965
Gene description
NF1 (neurofibromin 1) promoter region
Gene type
biological region
Feature type(s)
misc_feature: conserved_region
protein_bind
regulatory: enhancer, promoter, silencer, transcriptional_cis_regulatory_region
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 and associated regulatory elements of the neurofibromin 1 gene. It includes a sequence downstream of the start of transcription that dampens promoter activity. This promoter is stimulated by binding of cAMP responsive element binding protein 1 and Sp1 transcription factor. Spi-1 proto-oncogene, Irf2, and Irf8 form a complex on a conserved sequence element that promotes transcription in differentiated myeloid cells. Runx1, CCAAT/enhancer binding protein alpha, and Ets2 also positively regulate this promoter. Cytosine methylation of this genomic region was not found to a be associated with gene inactivation in tumor cells. However, methylation of specific transcription factor binding sites might affect transcription factor binding and thereby influence promoter activity. This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (31093605..31095381)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (32039338..32041115)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (29420623..29422384)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SMAD specific E3 ubiquitin protein ligase 2 (SMURF2) pseudogene Neighboring gene NF1-REPb PRS3 recombination region Neighboring gene leucine rich repeat containing 37B pseudogene Neighboring gene uncharacterized LOC124903974 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:29430681-29430862 Neighboring gene MIR4733 host gene Neighboring gene microRNA 4733 Neighboring gene neurofibromin 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:29471062-29471656 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:29471657-29472252 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:29472253-29472846 Neighboring gene NF1 intron 1 Alu-mediated recombination region Neighboring gene NF1 intron 2 Alu-mediated recombination region Neighboring gene NF1 intron 3 Alu-mediated recombination region Neighboring gene NF1 intron 8 Alu-mediated recombination region Neighboring gene uncharacterized LOC101927057 Neighboring gene oligodendrocyte myelin glycoprotein

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. Analysis of NF1 transcriptional regulatory elements. Lee TK, et al. Am J Med Genet A, 2005 Aug 30. PMID 16059932
  2. No aberrant methylation of neurofibromatosis 1 gene (NF1) promoter in pilocytic astrocytoma in childhood. Ebinger M, et al. Pediatr Hematol Oncol, 2005 Jan-Feb. PMID 15770836
  3. Analysis of somatic NF1 promoter methylation in plexiform neurofibromas and Schwann cells. Fishbein L, et al. Cancer Genet Cytogenet, 2005 Mar. PMID 15721644
  4. Methylation analysis of the neurofibromatosis type 1 (NF1) promoter in peripheral nerve sheath tumours. Harder A, et al. Eur J Cancer, 2004 Dec. PMID 15571966
  5. Microsatellite instability and promoter methylation as possible causes of NF1 gene inactivation in neurofibromas. Luijten M, et al. Eur J Hum Genet, 2000 Dec. PMID 11175282

See all (19) citations in PubMed

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 8408
  • ATAC-STARR-seq lymphoblastoid silent region 8409

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_056197.2 

    Range
    101..1877
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    31093605..31095381
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791803.1 Reference GRCh38.p14 PATCHES

    Range
    172779..174555
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    32039338..32041115
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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