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LOC121392912 Sharpr-MPRA regulatory region 9889 [ Homo sapiens (human) ]

Gene ID: 121392912, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121392912
Gene description
Sharpr-MPRA regulatory region 9889
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region). This locus also represents an accessible chromatin region that was validated as a silencer based on its ability to repress 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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See LOC121392912 in Genome Data Viewer
Location:
11p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47269895..47270424)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47426665..47427195)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47291446..47291975)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:47236089-47237288 Neighboring gene damage specific DNA binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4694 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47270641-47270808 Neighboring gene acid phosphatase 2, lysosomal Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47280987-47281555 Neighboring gene nuclear receptor subfamily 1 group H member 3 Neighboring gene Sharpr-MPRA regulatory region 2100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3325 Neighboring gene MADD antisense RNA 1 Neighboring gene MAP kinase activating death domain Neighboring gene myosin binding protein C3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47371915-47372896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47372897-47373877

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 silent region 3326

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_074569.2 

    Range
    101..630
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    47269895..47270424
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    47426665..47427195
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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