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LOC106736614 RET 5' regulatory region [ Homo sapiens (human) ]

Gene ID: 106736614, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106736614
Gene description
RET 5' regulatory region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: enhancer, promoter
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region contains upstream regulatory elements for the ret proto-oncogene (RET), including multiple enhancers and the proximal promoter. The distal enhancer is activated by synergistic binding of SRY box 10 and paired box 3. Signaling by retinoic acid displaces chromatin repressors (e.g. methyl CpG binding protein 2, histone deacetylase 1) from this region, thereby potentiating activity of the downstream promoter. The more proximal regulatory elements are positively regulated by homeobox B5, NK2 homeobox 1, and paired-like homeobox 2b, and negatively regulated by early growth response 1 (Egr1). Two common polymorphisms (rs10900296 and rs10900297) in this region are associated with risk of Hirschsprung disease and disrupt the recognition site of NK2 homeobox 1. A subregion was also shown to be an enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Dec 2022]
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Genomic context

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Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (43072914..43077291)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (43950387..43954764)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (43568362..43572739)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs2497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43483113-43483758 Neighboring gene long intergenic non-protein coding RNA 1264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43485513-43486245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43492878-43493378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43495973-43496668 Neighboring gene microRNA 5100 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:43507236-43508231 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:43508232-43509226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43521134-43521642 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:43521643-43522150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43522661-43523168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43535603-43536323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43539799-43540690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43540691-43541582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43544190-43544720 Neighboring gene VISTA enhancer hs2498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43557619-43558120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43558121-43558620 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:43572872-43573862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43580156-43580656 Neighboring gene VISTA enhancer hs2326 Neighboring gene RET intron 1 enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43596873-43597372 Neighboring gene ret proto-oncogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43600219-43600970 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3282 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:43604510-43604673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3286 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:43625782-43626382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43626383-43626983 Neighboring gene CSGALNACT2 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2318 Neighboring gene chondroitin sulfate N-acetylgalactosaminyltransferase 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:43655229-43656428 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12290

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

  • H3K4me1 hESC enhancer GRCh37_chr10:43571706-43572563

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_045003.1 

    Range
    101..4478
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    43072914..43077291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    43950387..43954764
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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