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LOC123480933 Sharpr-MPRA regulatory region 780 [ Homo sapiens (human) ]

Gene ID: 123480933, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123480933
Gene description
Sharpr-MPRA regulatory region 780
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (128683314..128683608)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (131987517..131987811)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (129604469..129604763)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21891 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129487118-129487618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129487619-129488119 Neighboring gene uncharacterized LOC124900778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129535873-129536374 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129536375-129536874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:129560764-129561264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129565349-129565848 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:129569028-129569766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129573717-129574216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21893 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:129603876-129604400 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129605286-129606025 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:129606954-129608153 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129613233-129613734 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74071 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74072 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129655317-129655816 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:129654815-129655316 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG hESC enhancer GRCh37_chr4:129697052-129697573 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129723780-129724699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129734111-129734692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:129734693-129735274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21898 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:129752609-129753288 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:129753289-129753968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:129756920-129757462 Neighboring gene jade family PHD finger 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21899 Neighboring gene sodium channel and clathrin linker 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_077627.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    128683314..128683608
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    131987517..131987811
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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