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LOC122756385 Sharpr-MPRA regulatory region 966 [ Homo sapiens (human) ]

Gene ID: 122756385, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122756385
Gene description
Sharpr-MPRA regulatory region 966
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 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 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Sep 2021]
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Genomic context

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Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (15043725..15044019)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (15074473..15074767)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (15183849..15184143)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 276 Neighboring gene RNA, U6 small nuclear 1288, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:14472914-14473113 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:14541927-14542484 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:14654042-14654593 Neighboring gene LRAT domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:14988479-14989049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11184 Neighboring gene NBAS subunit of NRZ tethering complex Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:15100270-15101469 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr2:15182798-15183298 and GRCh37_chr2:15183299-15183799 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15213063-15213219 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:15224708-15225393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:15225394-15226078 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:15281925-15283124 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15315340-15315550 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:15399317-15400143 Neighboring gene NANOG hESC enhancer GRCh37_chr2:15589330-15589831 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15606309-15606502 Neighboring gene ribosomal protein S26 pseudogene 18 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15672530-15672745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15346 Neighboring gene uncharacterized LOC105373440

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_076874.1 

    Range
    101..395
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    15043725..15044019
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    15074473..15074767
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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