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LOC124629338 Sharpr-MPRA regulatory region 4473 [ Homo sapiens (human) ]

Gene ID: 124629338, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124629338
Gene description
Sharpr-MPRA regulatory region 4473
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, 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 (28191616..28191910)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (28063718..28064011)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4316 Neighboring gene IFT57 pseudogene 1 Neighboring gene uncharacterized LOC729291 Neighboring gene MPRA-validated peak1636 silencer Neighboring gene coiled-coil domain containing 91 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27354 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6155 Neighboring gene MPRA-validated peak1637 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27393 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27419 Neighboring gene RNA, U4 small nuclear 54, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27646 Neighboring gene RNA, 5S ribosomal pseudogene 355

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_079617.1 

    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
    28191616..28191910
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    28063718..28064011
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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