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LOC121725147 Sharpr-MPRA regulatory region 12039 [ Homo sapiens (human) ]

Gene ID: 121725147, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725147
Gene description
Sharpr-MPRA regulatory region 12039
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121725147 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (58585362..58585656)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (58625744..58626038)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (58571089..58571383)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58506479-58506996 Neighboring gene acyl-CoA oxidase 2 Neighboring gene ribosomal protein L27 pseudogene 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58512267-58512782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58516141-58516641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58517009-58517510 Neighboring gene uncharacterized LOC107984079 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58546021-58547021 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58547022-58547522 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58547523-58548023 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58548024-58549024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58551424-58551948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58551949-58552472 Neighboring gene family with sequence similarity 107 member A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20013 Neighboring gene FAM3D antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:58602944-58603149 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:58614585-58615086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58626158-58626658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58626659-58627159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58634821-58635320 Neighboring gene FAM3 metabolism regulating signaling molecule D Neighboring gene uncharacterized LOC105377109

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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)

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_075616.1 

    Range
    101..395
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    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
    58585362..58585656
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    58625744..58626038
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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