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LOC124625885 Sharpr-MPRA regulatory region 1542 [ Homo sapiens (human) ]

Gene ID: 124625885, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625885
Gene description
Sharpr-MPRA regulatory region 1542
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [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 (3300763..3301057)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (3307237..3307531)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene tetraspanin 9 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3323859-3324398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3336210-3336725 Neighboring gene uncharacterized LOC124902861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3340427-3341425 Neighboring gene ribosomal protein S27 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3344565-3345246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3345247-3345928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3351329-3352214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3352304-3352804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3373093-3373682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3373683-3374271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3393392-3393892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3393893-3394393 Neighboring gene uncharacterized LOC100128253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5817 Neighboring gene long intergenic non-protein coding RNA 2827 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:3421757-3422956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4140 Neighboring gene tetraspanin 11 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3435715-3436214 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:3443867-3445066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3474236-3474788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3474789-3475339 Neighboring gene long intergenic non-protein coding RNA 2417

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_079485.1 

    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
    3300763..3301057
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    3307237..3307531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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