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LOC123620125 Sharpr-MPRA regulatory region 9341 [ Homo sapiens (human) ]

Gene ID: 123620125, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620125
Gene description
Sharpr-MPRA regulatory region 9341
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 Sharpr-MPRA (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 25:Art, potential CNV or repetitive artifacts). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (44096752..44097046)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (43930212..43930506)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (44064489..44064783)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA polymerase I and III subunit C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43972319-43972950 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:43977969-43979168 Neighboring gene long intergenic non-protein coding RNA 3040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44007317-44008074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44009776-44010524 Neighboring gene Sharpr-MPRA regulatory region 2143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44019358-44019952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44022316-44022816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17245 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44030458-44031420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24630 Neighboring gene stem cell inhibitory RNA transcript Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91788 Neighboring gene Sharpr-MPRA regulatory region 15428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44069931-44070480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44070481-44071029 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91802 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44075151-44075650 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91827 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91835 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17251 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:44098898-44099057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44100902-44101867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44101868-44102832 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91847 Neighboring gene ribosomal protein L29 pseudogene 16 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91852 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91874 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91884 Neighboring gene uncharacterized LOC107986599 Neighboring gene transmembrane protein 63B Neighboring gene mitochondrial ribosomal protein L14

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 17249

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_078109.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    44096752..44097046
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    43930212..43930506
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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