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LOC122889072 Sharpr-MPRA regulatory region 106 [ Homo sapiens (human) ]

Gene ID: 122889072, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889072
Gene description
Sharpr-MPRA regulatory region 106
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 non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889072 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 (40458838..40459132)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (40473911..40474205)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (40500329..40500623)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene phosphoglycerate mutase 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14231 Neighboring gene ENTPD3 antisense RNA 1 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:40459610-40459810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19717 Neighboring gene Sharpr-MPRA regulatory region 7904 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14232 Neighboring gene ribosomal protein L14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19718 Neighboring gene zinc finger protein 619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:40534545-40535044 Neighboring gene RNA, U5B small nuclear 2, pseudogene

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_077206.1 

    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
    40458838..40459132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    40473911..40474205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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