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LOC106728414 POMC distal enhancer region [ Homo sapiens (human) ]

Gene ID: 106728414, updated on 13-Mar-2024

Summary

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Gene symbol
LOC106728414
Gene description
POMC distal enhancer region
Gene type
biological region
Feature type(s)
misc_feature: conserved_region
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
nPE1; nPE2
Summary
This region contains two conserved sequences and functions as a neuronal enhancer of the POMC (proopiomelanocortin) gene, located approximately 10 kb downstream. The nPE1 element is distantly related to an MaLR family retroelement, while the nPE2 element is related to an ancient family of SINE elements. Two subregions marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. The mouse orthologs of these elements can each function as enhancers in the hypothalamic neurons, despite lacking significant sequence identity. Thus, these elements are an example of retroelement exaptation followed by convergent evolution of function. [provided by RefSeq, Oct 2022]
Orthologs
mouse all
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Genomic context

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Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (25176931..25179686)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (25211405..25214162)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (25399800..25402555)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene EFR3 homolog B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25311273-25312272 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:25312273-25313271 Neighboring gene SUCLA2 pseudogene 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:25320574-25320751 Neighboring gene Sharpr-MPRA regulatory region 3202 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_58220 Neighboring gene Sharpr-MPRA regulatory region 11705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25359725-25360226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25360227-25360726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25383210-25384066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11244 Neighboring gene POMC promoter region Neighboring gene proopiomelanocortin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25439263-25439780 Neighboring gene long intergenic non-protein coding RNA 1381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25452372-25453102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25469436-25469945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25470965-25471472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25476274-25476808 Neighboring gene DNA methyltransferase 3 alpha Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25482555-25483258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25486869-25487452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25487453-25488037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25492834-25493424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25495919-25496419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25499151-25499742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25500333-25500922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25500923-25501512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15446 Neighboring gene Sharpr-MPRA regulatory region 14395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25519631-25520132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25528466-25528966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25528967-25529467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25531317-25531818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25531819-25532318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25535893-25536656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25536657-25537420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25544961-25545788 Neighboring gene microRNA 1301

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. Positive selection of co-opted mobile genetic elements in a mammalian gene: If you can't beat them, join them. Franchini LF, et al. Mob Genet Elements, 2012 Mar 1. PMID 22934245, Free PMC Article
  2. Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons. Franchini LF, et al. Proc Natl Acad Sci U S A, 2011 Sep 13. PMID 21876128, Free PMC Article
  3. Regulation of proopiomelanocortin gene expression: an overview of the signaling cascades, transcription factors, and responsive elements involved. Jenks BG. Ann N Y Acad Sci, 2009 Apr. PMID 19456325
  4. Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. Santangelo AM, et al. PLoS Genet, 2007 Oct. PMID 17922573, Free PMC Article
  5. Identification of neuronal enhancers of the proopiomelanocortin gene by transgenic mouse analysis and phylogenetic footprinting. de Souza FS, et al. Mol Cell Biol, 2005 Apr. PMID 15798195, Free PMC Article

See all (6) 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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Homology

Other Names

  • H3K4me1 hESC enhancer GRCh37_chr2:25401427-25401928
  • H3K4me1 hESC enhancer GRCh37_chr2:25401929-25402428
  • POMC nPE1, nPE2 enhancer region

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_044976.1 

    Range
    101..2856
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    25176931..25179686
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    25211405..25214162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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