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LOC124855076 Sharpr-MPRA regulatory region 2624 [ Homo sapiens (human) ]

Gene ID: 124855076, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124855076
Gene description
Sharpr-MPRA regulatory region 2624
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, Apr 2022]
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Genomic context

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Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (32139332..32139626)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (31356537..31356831)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900336 Neighboring gene uncharacterized LOC124903149 Neighboring gene eukaryotic translation elongation factor 1 delta pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:32519515-32520016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:32520017-32520516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7553 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5244 Neighboring gene Sharpr-MPRA regulatory region 10155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5245 Neighboring gene FRY antisense RNA 1 Neighboring gene FRY microtubule binding protein Neighboring gene NANOG hESC enhancer GRCh37_chr13:32716946-32717447 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:32739396-32740595 Neighboring gene Sharpr-MPRA regulatory region 7321 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:32784277-32785476 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:32827763-32828962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5247 Neighboring gene BRCA2 promoter/silencer region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7554 Neighboring gene zygote arrest 1 like Neighboring gene BRCA2 DNA repair associated Neighboring gene Sharpr-MPRA regulatory region 1962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7555 Neighboring gene interferon induced protein with tetratricopeptide repeats 1 pseudogene 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_079958.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    32139332..32139626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    31356537..31356831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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