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LOC123493259 Sharpr-MPRA regulatory region 13256 [ Homo sapiens (human) ]

Gene ID: 123493259, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123493259
Gene description
Sharpr-MPRA regulatory region 13256
Gene type
biological region
Feature type(s)
regulatory: silencer
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 repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123493259 in Genome Data Viewer
Location:
5p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (1276694..1276988)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (1183622..1183916)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (1276809..1277103)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1204178-1204741 Neighboring gene solute carrier family 6 member 19 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1225890-1226432 Neighboring gene solute carrier family 6 member 18 Neighboring gene MNS16A minisatellite promoter Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1264322-1264939 Neighboring gene telomerase reverse transcriptase Neighboring gene TERT enhancer in intron 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1290609-1291360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1291361-1292111 Neighboring gene TERT 5' regulatory region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22306 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22307 Neighboring gene microRNA 4457 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:1320136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1325297-1325797 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:1327650-1328264 Neighboring gene CLPTM1 like Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:1328265-1328877 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:1330840 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:1341101

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_077683.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    1276694..1276988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    1183622..1183916
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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