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LOC123477727 Sharpr-MPRA regulatory region 10943 [ Homo sapiens (human) ]

Gene ID: 123477727, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123477727
Gene description
Sharpr-MPRA regulatory region 10943
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (37873468..37873762)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (37842550..37842844)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (37875089..37875383)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:37827979-37828480 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:37828481-37828980 Neighboring gene phosphoglucomutase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:37882909-37883409 Neighboring gene heterogeneous nuclear ribonucleoprotein R pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21417 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:37901172-37901710 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:37902885-37903448 Neighboring gene TBC1 domain family member 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:37955381-37956580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15355 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21419 Neighboring gene pituitary tumor-transforming 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_79216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21420 Neighboring gene proteasome activator subunit 2 pseudogene 4

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_077530.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    37873468..37873762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    37842550..37842844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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