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LOC123477806 Sharpr-MPRA regulatory region 3285 [ Homo sapiens (human) ]

Gene ID: 123477806, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123477806
Gene description
Sharpr-MPRA regulatory region 3285
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 unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123477806 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (112213233..112213527)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (115521590..115521884)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (113134389..113134683)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21820 Neighboring gene family with sequence similarity 241 member A Neighboring gene ribosomal protein L36a pseudogene 19 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:113152716-113153663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15636 Neighboring gene AP1AR divergent transcript Neighboring gene adaptor related protein complex 1 associated regulatory protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15637 Neighboring gene TRAF interacting protein with forkhead associated domain

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_077609.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    112213233..112213527
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    115521590..115521884
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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