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LOC123881360 Sharpr-MPRA regulatory region 9625 [ Homo sapiens (human) ]

Gene ID: 123881360, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123881360
Gene description
Sharpr-MPRA regulatory region 9625
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [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 (163579217..163579511)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (164944322..164944616)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (164000249..164000543)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene basic proline-rich protein-like Neighboring gene H3K27ac hESC enhancers GRCh37_chr6:163835002-163835654 and GRCh37_chr6:163835655-163836308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17772 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:163844209-163844453 Neighboring gene colon adenocarcinoma hypermethylated Neighboring gene QKI, KH domain containing RNA binding Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25419 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:163956589-163956770 Neighboring gene NANOG hESC enhancer GRCh37_chr6:163964125-163964810 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:164008464-164009663 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:164013504-164014052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:164032378-164032878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:164032879-164033379 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:164039878-164041077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25420 Neighboring gene uncharacterized LOC102724152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25423 Neighboring gene uncharacterized LOC124901498

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_078265.1 

    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
    163579217..163579511
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    164944322..164944616
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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