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LOC123497943 Sharpr-MPRA regulatory region 4368 [ Homo sapiens (human) ]

Gene ID: 123497943, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123497943
Gene description
Sharpr-MPRA regulatory region 4368
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 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_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (96963325..96963619)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (97464204..97464498)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (96299029..96299323)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene endoplasmic reticulum aminopeptidase 1 Neighboring gene uncharacterized LOC124901030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22829 Neighboring gene ribosomal protein S20 pseudogene 16 Neighboring gene leucyl and cystinyl aminopeptidase Neighboring gene MPRA-validated peak5362 silencer Neighboring gene Sharpr-MPRA regulatory region 9279 Neighboring gene SET pseudogene 22 Neighboring gene LIX1 and RIOK2 antisense RNA 1 Neighboring gene limb and CNS expressed 1

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_077796.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    96963325..96963619
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    97464204..97464498
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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