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LOC113875006 Sharpr-MPRA regulatory region 4636 [ Homo sapiens (human) ]

Gene ID: 113875006, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875006
Gene description
Sharpr-MPRA regulatory region 4636
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 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 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). In addition, this genomic region was validated as a cis-regulatory element for the TMSB4X (thymosin beta 4 X-linked) gene on chromosome X based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
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Genomic context

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Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (12950170..12950582)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (12531635..12532047)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (12968289..12968701)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29414 Neighboring gene toll like receptor 7 Neighboring gene Sharpr-MPRA regulatory region 5588 Neighboring gene TLR8 antisense RNA 1 Neighboring gene toll like receptor 8 Neighboring gene CRISPRi-validated cis-regulatory element chrX.229 Neighboring gene CRISPRi-validated cis-regulatory element chrX.231 Neighboring gene CRISPRi-validated cis-regulatory element chrX.232 Neighboring gene CRISPRi-validated cis-regulatory element chrX.233 Neighboring gene CRISPRi-validated cis-regulatory element chrX.234 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:12982027-12982688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29422 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:12992269-12993108 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:12993948-12994786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29423 Neighboring gene CRISPRi-validated cis-regulatory element chrX.239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29424 Neighboring gene CRISPRi-validated cis-regulatory element chrX.240 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:13005300-13005496 Neighboring gene thymosin beta 4 X-linked Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29427 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29430 Neighboring gene family with sequence similarity 9 member C

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. 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)

General gene information

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Other Names

  • CRISPRi-validated cis-regulatory element chrX.230

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_063194.2 

    Range
    101..513
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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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    12950170..12950582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    12531635..12532047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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