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LOC123620093 Sharpr-MPRA regulatory region 4993 [ Homo sapiens (human) ]

Gene ID: 123620093, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620093
Gene description
Sharpr-MPRA regulatory region 4993
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123620093 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (35185332..35185626)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (35008402..35008696)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (35153109..35153403)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ankyrin repeat and sterile alpha motif domain containing 1A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24394 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 11 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35012271-35012922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35015552-35016400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35016401-35017247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35025703-35026222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35027261-35027778 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35036049-35036712 Neighboring gene NANOG hESC enhancer GRCh37_chr6:35037908-35038409 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35049025-35049696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35054004-35054504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35055243-35056070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35056071-35056896 Neighboring gene MPRA-validated peak5763 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24395 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:35115441-35116234 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:35116235-35117028 Neighboring gene MPRA-validated peak5764 silencer Neighboring gene t-complex 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35152333-35152714 Neighboring gene uncharacterized LOC112267955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17084 Neighboring gene SCUBE3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 1078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17085 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:35211069-35212268 Neighboring gene signal peptide, CUB domain and EGF like domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24396

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_078077.1 

    Range
    101..395
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    35185332..35185626
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    35008402..35008696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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