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LOC123480943 Sharpr-MPRA regulatory region 7410 [ Homo sapiens (human) ]

Gene ID: 123480943, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123480943
Gene description
Sharpr-MPRA regulatory region 7410
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 non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123480943 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (140884495..140884789)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (144204323..144204617)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (141805649..141805943)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene TBC1 domain family member 9 Neighboring gene uncharacterized LOC124900787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21936 Neighboring gene uncharacterized LOC124900786 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:141677237-141677879 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:141677880-141678521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:141746857-141747378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:141747379-141747899 Neighboring gene ring finger protein 150 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:141972205-141972434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15715 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:142141834-142142340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:142142341-142142845 Neighboring gene zinc finger protein 330 Neighboring gene small nucleolar RNA U13

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_077637.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    140884495..140884789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    144204323..144204617
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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