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LOC123497920 Sharpr-MPRA regulatory region 2636 [ Homo sapiens (human) ]

Gene ID: 123497920, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123497920
Gene description
Sharpr-MPRA regulatory region 2636
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123497920 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (80184327..80184621)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (80668205..80668499)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (79480149..79480443)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene thrombospondin 4 Neighboring gene tRNA methyltransferase subunit 11-2 pseudogene 2 Neighboring gene MPRA-validated peak5305 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:79366012-79367211 Neighboring gene THBS4 antisense RNA 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:79374873-79376072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16133 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:79380002-79380216 Neighboring gene Sharpr-MPRA regulatory region 11102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16135 Neighboring gene serine incorporator 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:79441323-79441824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:79447797-79448296 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:79454739-79455715 Neighboring gene Sharpr-MPRA regulatory region 551 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:79481420-79482241 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79483381-79484211 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:79487586-79488157 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:79488158-79488728 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:79489301-79489871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79493799-79494363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79494364-79494927 Neighboring gene small nucleolar RNA U13 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79541871-79542373 Neighboring gene Sharpr-MPRA regulatory region 10230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:79545029-79545596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16136 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79552033-79552966 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79552967-79553900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79553901-79554832 Neighboring gene Sharpr-MPRA regulatory region 10881 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:79568395-79568638 Neighboring gene keratin 18 pseudogene 45

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_077774.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    80184327..80184621
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    80668205..80668499
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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