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LOC123493232 Sharpr-MPRA regulatory region 10828 [ Homo sapiens (human) ]

Gene ID: 123493232, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123493232
Gene description
Sharpr-MPRA regulatory region 10828
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 DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123493232 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (159341477..159341771)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (162692254..162692548)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (160262629..160262923)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene sperm microtubule inner protein 2 Neighboring gene fatty acid binding protein 5 pseudogene 12 Neighboring gene Sharpr-MPRA regulatory region 3178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22089 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:160023381-160024072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15775 Neighboring gene Sharpr-MPRA regulatory region 13777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15777 Neighboring gene Rap guanine nucleotide exchange factor 2 Neighboring gene Sharpr-MPRA regulatory region 8742 Neighboring gene microRNA 3688-1 Neighboring gene microRNA 3688-2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22090 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:160096538-160097270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22092 Neighboring gene Sharpr-MPRA regulatory region 9369 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:160304254-160304828 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:160304829-160305402 Neighboring gene MPRA-validated peak5139 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:160322475-160323674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22093 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15778 Neighboring gene uncharacterized LOC124900924 Neighboring gene uncharacterized LOC124900926

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_077656.1 

    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
    159341477..159341771
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    162692254..162692548
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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