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LOC123775378 Sharpr-MPRA regulatory region 1235 [ Homo sapiens (human) ]

Gene ID: 123775378, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123775378
Gene description
Sharpr-MPRA regulatory region 1235
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, Jan 2022]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (82264912..82265206)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (83484355..83484649)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (82974629..82974923)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2542 Neighboring gene Sharpr-MPRA regulatory region 11142 Neighboring gene uncharacterized LOC107986617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24776 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:82853903-82855102 Neighboring gene MPRA-validated peak5922 silencer Neighboring gene inhibitor of Bruton tyrosine kinase Neighboring gene RNA, U6 small nuclear 130, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr6:82949825-82950342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17353 Neighboring gene single stranded DNA binding protein 2 pseudogene Neighboring gene uncharacterized LOC105377874 Neighboring gene MPRA-validated peak5923 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24778 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:82999144-82999335 Neighboring gene uncharacterized LOC105377875 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:83072967-83073480 Neighboring gene trophoblast glycoprotein

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_078146.1 

    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
    82264912..82265206
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_013171802.1 Reference GRCh38.p14 PATCHES

    Range
    134727..135021
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    83484355..83484649
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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