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LOC122965322 Sharpr-MPRA regulatory region 8400 [ Homo sapiens (human) ]

Gene ID: 122965322, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122965322
Gene description
Sharpr-MPRA regulatory region 8400
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, Oct 2021]
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Genomic context

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See LOC122965322 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (62538714..62539008)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (62582298..62582592)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (62524389..62524683)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:62354716-62355621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:62357949-62358508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:62358509-62359066 Neighboring gene VISTA enhancer hs435 Neighboring gene uncharacterized LOC105377647 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:62362229-62362828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:62362829-62363426 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:62400506-62401328 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:62401329-62402151 Neighboring gene FEZ family zinc finger 2 Neighboring gene VISTA enhancer hs1316 Neighboring gene calcium dependent secretion activator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:62523426-62524136 Neighboring gene Sharpr-MPRA regulatory region 14545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20030 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:62654458-62654958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:62654959-62655459 Neighboring gene ribosomal protein L14 pseudogene 2 Neighboring gene RNA, 7SL, cytoplasmic 863, pseudogene

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_077241.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    62538714..62539008
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    62582298..62582592
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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