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LOC121853023 Sharpr-MPRA regulatory region 5316 [ Homo sapiens (human) ]

Gene ID: 121853023, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853023
Gene description
Sharpr-MPRA regulatory region 5316
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121853023 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (14578188..14578482)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (12933504..12933798)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (15950509..15950803)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18271 Neighboring gene heat shock protein family A (Hsp70) member 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18272 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:15821444-15821607 Neighboring gene CRISPRi-validated cis-regulatory element chr21.63 Neighboring gene CRISPRi-validated cis-regulatory element chr21.64 Neighboring gene uncharacterized LOC124905053 Neighboring gene SAM domain, SH3 domain and nuclear localization signals 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:15905912-15907111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13214 Neighboring gene SAMSN1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18276 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:15988445-15989206 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:15989207-15989967 Neighboring gene uncharacterized LOC105372738 Neighboring gene CRISPRi-validated cis-regulatory element chr21.70

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_076131.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    14578188..14578482
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    12933504..12933798
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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