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LOC123881327 Sharpr-MPRA regulatory region 942 [ Homo sapiens (human) ]

Gene ID: 123881327, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123881327
Gene description
Sharpr-MPRA regulatory region 942
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 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123881327 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (148868933..148869227)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (150068717..150069011)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (149190069..149190363)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17652 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17653 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149069303-149069804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149069805-149070304 Neighboring gene uncharacterized LOC107986659 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:149081854-149082604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25238 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:149090389-149091019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25239 Neighboring gene uronyl 2-sulfotransferase Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:149139935-149140821 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:149184983-149185492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17654 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:149194421-149195620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17655 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:149245080-149245698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:149284708-149285284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:149285285-149285861 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:149290736-149291326 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:149291327-149291917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:149293308-149294306 Neighboring gene UST antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr6:149301302-149301803 Neighboring gene uncharacterized LOC124901424

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_078232.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    148868933..148869227
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    150068717..150069011
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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