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LOC124625880 Sharpr-MPRA regulatory region 10568 [ Homo sapiens (human) ]

Gene ID: 124625880, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625880
Gene description
Sharpr-MPRA regulatory region 10568
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (1993463..1993757)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (1989579..1989875)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene calcium voltage-gated channel auxiliary subunit alpha2delta 4 Neighboring gene uncharacterized LOC124902858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2021735-2022235 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2025891-2026467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2042322-2042920 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:2063223-2064422 Neighboring gene long intergenic non-protein coding RNA 940 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:2112705-2113344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5813 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:2120775-2121283 Neighboring gene decapping mRNA 1B Neighboring gene CACNA1C intronic transcript 1 Neighboring gene calcium voltage-gated channel subunit alpha1 C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4127 Neighboring gene CACNA1C intronic transcript 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

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_079480.1 

    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
    1993463..1993757
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654718.1 Reference GRCh38.p14 PATCHES

    Range
    335607..335901
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    1989579..1989875
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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