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LOC125424394 Sharpr-MPRA regulatory region 8041 [ Homo sapiens (human) ]

Gene ID: 125424394, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125424394
Gene description
Sharpr-MPRA regulatory region 8041
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125424394 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (23565282..23565576)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (24012499..24012793)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (23907469..23907763)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:23871859-23872474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:23874941-23875556 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:23876790-23877405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:23877406-23878022 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:23878638-23879254 Neighboring gene endogenous retrovirus group K member 5 Gag polyprotein-like Neighboring gene Sharpr-MPRA regulatory region 4313 Neighboring gene Sharpr-MPRA regulatory regions 962 and 2236 Neighboring gene prostate cancer associated transcript 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:23891199-23891699 Neighboring gene uncharacterized LOC105372957 Neighboring gene immunoglobulin lambda like polypeptide 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

See Variation Viewer (GRCh37.p13)

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_081129.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    23565282..23565576
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    24012499..24012793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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