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LOC122861280 Sharpr-MPRA regulatory region 7917 [ Homo sapiens (human) ]

Gene ID: 122861280, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861280
Gene description
Sharpr-MPRA regulatory region 7917
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 Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes an accessible chromatin subregion 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 LOC122861280 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (206084905..206085199)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (206566794..206567088)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (206949629..206949923)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene peptidylprolyl isomerase A pseudogene 68 Neighboring gene MPRA-validated peak4024 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:206868888-206869466 Neighboring gene INO80 complex subunit D Neighboring gene ribosomal protein L27 pseudogene 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:206946709-206947498 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:206948195-206949016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12263 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12265 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:206950661-206951480 Neighboring gene INO80D antisense RNA 1 Neighboring gene NADH:ubiquinone oxidoreductase core subunit S1 Neighboring gene GCSH pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12266 Neighboring gene small nucleolar RNA, C/D box 51 Neighboring gene eukaryotic translation elongation factor 1 beta 2

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 silent region 12262

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_077096.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    206084905..206085199
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_015495299.1 Reference GRCh38.p14 PATCHES

    Range
    193923..194217
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    206566794..206567088
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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