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LOC123620124 Sharpr-MPRA regulatory region 5169 [ Homo sapiens (human) ]

Gene ID: 123620124, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620124
Gene description
Sharpr-MPRA regulatory region 5169
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 matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123620124 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (43807592..43807886)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (43637096..43637390)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (43775329..43775623)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA polymerase I and III subunit C Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:43674891-43675733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24614 Neighboring gene Sharpr-MPRA regulatory region 12588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24615 Neighboring gene EXOSC8 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43726130-43726666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43728022-43728522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43728523-43729023 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43732509-43733010 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17241 Neighboring gene H3K27ac hESC enhancers GRCh37_chr6:43738373-43739138 and GRCh37_chr6:43739139-43739904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43740671-43741436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43739905-43740670 Neighboring gene Sharpr-MPRA regulatory region 8365 Neighboring gene uncharacterized LOC105375070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43766999-43767583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24620 Neighboring gene uncharacterized LOC105375069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43818433-43819079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43819080-43819726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43819727-43820373 Neighboring gene vascular endothelial growth factor A Neighboring gene long intergenic non-protein coding RNA 2537

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_078108.1 

    Range
    101..395
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    43807592..43807886
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    43637096..43637390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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