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LOC123480920 Sharpr-MPRA regulatory region 13729 [ Homo sapiens (human) ]

Gene ID: 123480920, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123480920
Gene description
Sharpr-MPRA regulatory region 13729
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 16:ElonW, transcriptional elongation, weaker H3K36me3). [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 (113593453..113593747)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (116902191..116902485)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (114514609..114514903)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377374 Neighboring gene RNA, 7SL, cytoplasmic 184, pseudogene Neighboring gene RNA, U1 small nuclear 138, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:114373445-114373992 Neighboring gene calcium/calmodulin dependent protein kinase II delta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15645 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72235 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:114481688-114482887 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15646 Neighboring gene Sharpr-MPRA regulatory region 15168 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:114566848-114567352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21838 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15647 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:114683084-114683622 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:114683623-114684161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21839 Neighboring gene uncharacterized LOC105377375 Neighboring gene NANOG hESC enhancer GRCh37_chr4:114805704-114806205 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:114839688-114840887 Neighboring gene arylsulfatase family member J

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_077614.1 

    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
    113593453..113593747
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    116902191..116902485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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