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LOC122889059 Sharpr-MPRA regulatory region 9798 [ Homo sapiens (human) ]

Gene ID: 122889059, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889059
Gene description
Sharpr-MPRA regulatory region 9798
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889059 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 (30440977..30441271)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (30443383..30443677)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (30482469..30482763)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906224 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69363 Neighboring gene uncharacterized LOC124909358 Neighboring gene small nucleolar RNA U3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:30383595-30384794 Neighboring gene GATA motif-containing MPRA enhancer 299 Neighboring gene uncharacterized LOC101927995 Neighboring gene Sharpr-MPRA regulatory region 15230 Neighboring gene uncharacterized LOC105377013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19624 Neighboring gene long intergenic non-protein coding RNA 1985 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:30590862-30591747 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:30592706-30593238 Neighboring gene NANOG hESC enhancer GRCh37_chr3:30593324-30593858 Neighboring gene HNF1 motif-containing MPRA enhancer 129 Neighboring gene translation initiation factor IF-2-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14158 Neighboring gene transforming growth factor beta receptor 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

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_077191.1 

    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
    30440977..30441271
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    30443383..30443677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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