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LOC123477781 Sharpr-MPRA regulatory region 119 [ Homo sapiens (human) ]

Gene ID: 123477781, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123477781
Gene description
Sharpr-MPRA regulatory region 119
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 unmatched - State 1:Tss, active promoter, TSS/CpG island region). [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 (87007797..87008091)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (90337158..90337452)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (87928949..87929243)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene chromosome 4 open reading frame 36 Neighboring gene Sharpr-MPRA regulatory region 3757 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:87856539-87857080 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:87857081-87857622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:87861204-87861704 Neighboring gene AFF1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21697 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:87879079-87879662 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:87880372-87881044 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:87881045-87881716 Neighboring gene Sharpr-MPRA regulatory region 10323 Neighboring gene Sharpr-MPRA regulatory region 12874 Neighboring gene Sharpr-MPRA regulatory region 10097/5096 Neighboring gene ALF transcription elongation factor 1 Neighboring gene trans-2,3-enoyl-CoA reductase pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15553 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:87934257-87934756 Neighboring gene NANOG hESC enhancer GRCh37_chr4:87955092-87955593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:87958100-87958600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:87958601-87959101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15554 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:87960255-87961006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21701 Neighboring gene uncharacterized LOC105377320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:88041283-88041858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:88073576-88074076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:88074077-88074577 Neighboring gene uracil DNA glycosylase pseudogene Neighboring gene kelch like family member 8

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_077584.1 

    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
    87007797..87008091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    90337158..90337452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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