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LOC123881363 Sharpr-MPRA regulatory region 5298 [ Homo sapiens (human) ]

Gene ID: 123881363, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123881363
Gene description
Sharpr-MPRA regulatory region 5298
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 21:Repr, strong Polycomb repression). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123881363 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 (166718541..166718835)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (168096998..168097292)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (167132029..167132323)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S6 kinase A2 Neighboring gene uncharacterized LOC107986671 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:167068910-167069464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:167103273-167103941 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:167107051-167108250 Neighboring gene insulin like growth factor 2 mRNA binding protein 3 pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:167149720-167150919 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:167155940-167156108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:167179935-167180722 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:167184261-167185460 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:167196736-167197935 Neighboring gene uncharacterized LOC124901459 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:167250099-167250620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:167266611-167267589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17782 Neighboring gene MPRA-validated peak6317 silencer Neighboring gene uncharacterized LOC124901461

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_078268.1 

    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
    166718541..166718835
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    168096998..168097292
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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