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LOC124629391 Sharpr-MPRA regulatory region 4654 [ Homo sapiens (human) ]

Gene ID: 124629391, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124629391
Gene description
Sharpr-MPRA regulatory region 4654
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [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 (64694189..64694483)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (64673193..64673487)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Ras association domain family member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4624 Neighboring gene RASSF3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6597 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:65019275-65019991 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:65035223-65035726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65041527-65042250 Neighboring gene microRNA 548z Neighboring gene microRNA 548c Neighboring gene ReSE screen-validated silencer GRCh37_chr12:65046125-65046302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6600 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:65066263-65066452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65068096-65068875 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65151732-65152612 Neighboring gene glucosamine (N-acetyl)-6-sulfatase Neighboring gene small nucleolar RNA U13 Neighboring gene TBC1 domain family member 30

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_079754.1 

    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
    64694189..64694483
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    64673193..64673487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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