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LOC123497905 Sharpr-MPRA regulatory region 3458 [ Homo sapiens (human) ]

Gene ID: 123497905, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123497905
Gene description
Sharpr-MPRA regulatory region 3458
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (72245002..72245296)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (72726174..72726468)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (71540829..71541123)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379028 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:71403221-71404203 Neighboring gene Sharpr-MPRA regulatory region 7919 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:71418105-71418608 Neighboring gene microtubule associated protein 1B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:71453937-71454436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:71475503-71476092 Neighboring gene microRNA 4803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22644 Neighboring gene Sharpr-MPRA regulatory region 4397 Neighboring gene mitochondrial ribosomal protein S27 Neighboring gene uncharacterized LOC107986422 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:71597159-71598114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16079 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:71607834-71608334 Neighboring gene RNA, 7SL, cytoplasmic 153, pseudogene

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_077759.1 

    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
    72245002..72245296
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    72726174..72726468
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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