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LOC124646385 Sharpr-MPRA regulatory region 6189 [ Homo sapiens (human) ]

Gene ID: 124646385, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124646385
Gene description
Sharpr-MPRA regulatory region 6189
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [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 (96166291..96166585)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (96140422..96140716)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96465035-96465535 Neighboring gene YPEL5 pseudogene 3 Neighboring gene uncharacterized LOC105369923 Neighboring gene RNA, 7SL, cytoplasmic 88, pseudogene Neighboring gene long intergenic non-protein coding RNA 2452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6825 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96603880-96604402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6826 Neighboring gene uncharacterized LOC124902991 Neighboring gene ETS transcription factor ELK3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96628784-96629768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96631810-96632310 Neighboring gene cyclin dependent kinase 17 Neighboring gene RNA, U4 small nuclear 24, pseudogene

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_079793.1 

    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
    96166291..96166585
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    96140422..96140716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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