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LOC122889021 Sharpr-MPRA regulatory region 7157 [ Homo sapiens (human) ]

Gene ID: 122889021, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889021
Gene description
Sharpr-MPRA regulatory region 7157
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 16:ElonW, transcriptional elongation, weaker H3K36me3). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889021 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (4766745..4767039)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (4760597..4760891)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (4808429..4808723)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene inositol 1,4,5-trisphosphate receptor type 1 Neighboring gene uncharacterized LOC124906210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:4760598-4761098 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:4790473-4790665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19355 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:4824730-4825689 Neighboring gene eosinophil granule ontogeny transcript Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:4855759-4856958 Neighboring gene uncharacterized LOC124906209 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:4859780-4860166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:4866229-4866729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19360 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14019 Neighboring gene small nucleolar RNA U13 Neighboring gene BHLHE40 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:4947837-4948542 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:4958477-4959105 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:4987703-4987867 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:5021511-5022105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14021 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19362 Neighboring gene basic helix-loop-helix family member e40

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_077153.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    4766745..4767039
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    4760597..4760891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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