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LOC124629357 Sharpr-MPRA regulatory region 8177 [ Homo sapiens (human) ]

Gene ID: 124629357, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124629357
Gene description
Sharpr-MPRA regulatory region 8177
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (51320645..51320939)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (51283460..51283754)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51593597-51594096 Neighboring gene POU class 6 homeobox 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6373 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:51614127-51614306 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51631660-51632297 Neighboring gene Sharpr-MPRA regulatory region 9853 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51633573-51634209 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51641233-51641734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51641735-51642234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51642235-51642736 Neighboring gene DAZ associated protein 2 Neighboring gene small cell adhesion glycoprotein Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51663873-51664373 Neighboring gene bridging integrator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6376 Neighboring gene uncharacterized LOC105369767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4466 Neighboring gene Sharpr-MPRA regulatory region 12465 Neighboring gene chymotrypsin like elastase 1

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

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_079727.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    51320645..51320939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    51283460..51283754
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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