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LOC121853026 Sharpr-MPRA regulatory region 6397 [ Homo sapiens (human) ]

Gene ID: 121853026, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853026
Gene description
Sharpr-MPRA regulatory region 6397
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. A subregion was validated as a functional enhancer by Sharpr-MPRA (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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (33383006..33383477)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (31755251..31755722)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (34755489..34755783)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene IFNAR2-IL10RB readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18374 Neighboring gene interleukin 10 receptor subunit beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:34676441-34676940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13255 Neighboring gene IFNAR1 promoter region Neighboring gene interferon alpha and beta receptor subunit 1 Neighboring gene upstream transcription factor 1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 14728 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:34738709-34739908 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:34752348-34753547 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34758349-34758554 Neighboring gene IFNGR2 promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13259 Neighboring gene CRISPRi-FlowFISH-validated IFNGR2 regulatory element GRCh37_chr21:34776289-34777452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:34784507-34785261 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34785395-34785563 Neighboring gene interferon gamma receptor 2 Neighboring gene transmembrane protein 50B Neighboring gene RPS5 pseudogene 3

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 18379

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_076134.2 

    Range
    101..572
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    33383006..33383477
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    31755251..31755722
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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