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LOC124500690 Sharpr-MPRA regulatory regions 4651 and 6526 [ Homo sapiens (human) ]

Gene ID: 124500690, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124500690
Gene description
Sharpr-MPRA regulatory regions 4651 and 6526
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. Two overlapping subregions were validated as functional repressive elements by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays), where one subregion showed repressive activity in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin), while the other subregion showed repressive activity in K562 cells (group: K562 Repressive DNase matched - State 5:Enh). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124500690 in Genome Data Viewer
Location:
11q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (75406305..75406619)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (75335893..75336207)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (75117349..75117663)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75111125-75111988 Neighboring gene small nucleolar RNA, C/D box 15A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75118535-75119034 Neighboring gene small nucleolar RNA, C/D box 15B Neighboring gene ribosomal protein S3 Neighboring gene Sharpr-MPRA regulatory regions 6111 and 12908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3765 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75142886-75143772 Neighboring gene kelch like family member 35 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75151983-75152545 Neighboring gene glycerophosphodiester phosphodiesterase domain containing 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75167384-75167982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75171856-75172358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75177195-75177867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75178136-75178783 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75178784-75179430 Neighboring gene uncharacterized LOC105369389

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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 4651
  • Sharpr-MPRA regulatory region 6526

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_079349.1 

    Range
    101..415
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    75406305..75406619
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    75335893..75336207
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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