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LOC122128449 Sharpr-MPRA regulatory region 11922 [ Homo sapiens (human) ]

Gene ID: 122128449, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122128449
Gene description
Sharpr-MPRA regulatory region 11922
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 3:PromF, promoter flanking). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (157154157..157154451)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (156291002..156291296)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (157123949..157124243)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:157075101-157076062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1886 Neighboring gene ETS variant transcription factor 3 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:157082931-157083555 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:157083556-157084181 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:157107959-157108294 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:157108646-157109251 Neighboring gene CYCS pseudogene 52 Neighboring gene ETS variant transcription factor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:157127246-157127757 Neighboring gene Sharpr-MPRA regulatory region 527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:157142571-157143072 Neighboring gene uncharacterized LOC107985211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1887 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:157163574-157163806 Neighboring gene uncharacterized LOC105371456 Neighboring gene NANOG hESC enhancer GRCh37_chr1:157243171-157243713 Neighboring gene CRISPRi-validated cis-regulatory element chr1.9249 Neighboring gene long intergenic non-protein coding RNA 2772

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_076469.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    157154157..157154451
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    156291002..156291296
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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