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LOC122152353 Sharpr-MPRA regulatory region 1428 [ Homo sapiens (human) ]

Gene ID: 122152353, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122152353
Gene description
Sharpr-MPRA regulatory region 1428
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Aug 2021]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (243622007..243622301)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (243033160..243033454)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (243785309..243785603)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SHH signaling and ciliogenesis regulator SDCCAG8 Neighboring gene uncharacterized LOC124904569 Neighboring gene microRNA 4677 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:243617070-243618269 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:243639115-243639288 Neighboring gene Sharpr-MPRA regulatory region 5448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:243645455-243646070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:243647393-243647951 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:243653141-243653664 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:243653665-243654188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:243659455-243660106 Neighboring gene AKT serine/threonine kinase 3 Neighboring gene fatty acid binding protein 7 pseudogene 1 Neighboring gene VISTA enhancer hs545 Neighboring gene NANOG hESC enhancer GRCh37_chr1:243903627-243904128 Neighboring gene AKT3 intronic transcript 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_076619.1 

    Range
    101..395
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    243622007..243622301
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187519.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    634115..634409
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    243033160..243033454
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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