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LOC124188230 Sharpr-MPRA regulatory region 15510 [ Homo sapiens (human) ]

Gene ID: 124188230, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124188230
Gene description
Sharpr-MPRA regulatory region 15510
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 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124188230 in Genome Data Viewer
Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (127816743..127817037)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (128944231..128944525)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (128828989..128829283)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr8:128744882-128745383 Neighboring gene origin of replication upstream of MYC Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19530 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:128754894-128756093 Neighboring gene MYC proto-oncogene, bHLH transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128805180-128805750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19533 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128806893-128807462 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128807463-128808034 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128814781-128815422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128815423-128816064 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:128816065-128816704 Neighboring gene Sharpr-MPRA regulatory region 14038 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128821670-128822570 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128822571-128823470 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128830247-128830786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128832947-128833486 Neighboring gene microRNA 1204 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:128834567-128835106 Neighboring gene Pvt1 oncogene Neighboring gene ReSE screen-validated silencer GRCh37_chr8:128858753-128858938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128862019-128862636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128864303-128865152 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:128866418-128867617 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128879341-128879948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128888845-128889392 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:128891961-128892128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128893083-128893582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27951 Neighboring gene Sharpr-MPRA regulatory region 1737 Neighboring gene CRISPRi-validated MYC e1 enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128913423-128914077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128916503-128917004 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128920055-128920986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128920987-128921919 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:128923753-128924342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27953 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128932048-128932575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128936915-128937414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128951647-128952169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128969595-128970406 Neighboring gene CRISPRi-validated MYC e2 enhancer Neighboring gene long intergenic non-protein coding RNA 2912 Neighboring gene microRNA 1205

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_078706.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    127816743..127817037
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    128944231..128944525
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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