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LOC124625870 Sharpr-MPRA regulatory region 15352 [ Homo sapiens (human) ]

Gene ID: 124625870, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124625870
Gene description
Sharpr-MPRA regulatory region 15352
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124625870 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 (129881654..129881948)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (129917360..129917654)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (129751549..129751843)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902793 Neighboring gene Sharpr-MPRA regulatory region 8939 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:129673393-129673893 Neighboring gene transmembrane protein 45B Neighboring gene TMEM45B-NFRKB intergenic CAGE-defined mid-level expression enhancer Neighboring gene ReSE screen-validated silencer GRCh37_chr11:129739277-129739466 Neighboring gene nuclear factor related to kappaB binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4067 Neighboring gene PR/SET domain 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4068 Neighboring gene NANOG hESC enhancer GRCh37_chr11:129795831-129796332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:129806281-129806994 Neighboring gene MPRA-validated peak1509 silencer Neighboring gene Sharpr-MPRA regulatory region 3666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:129841453-129842000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4070 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4073 Neighboring gene CRISPRi-validated cis-regulatory element chr11.6035 Neighboring gene PRDM10 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4074 Neighboring gene elongin B pseudogene 2

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_079470.1 

    Range
    101..395
    Download
    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
    129881654..129881948
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    129917360..129917654
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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