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LOC122889044 Sharpr-MPRA regulatory region 448 [ Homo sapiens (human) ]

Gene ID: 122889044, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889044
Gene description
Sharpr-MPRA regulatory region 448
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, Oct 2021]
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Genomic context

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See LOC122889044 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (16659462..16659756)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (16660638..16660932)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (16700969..16701263)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 690 Neighboring gene deleted in azoospermia like Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16699444-16700249 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:16712625-16713593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16717988-16718488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16718489-16718989 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:16728537-16729494 Neighboring gene chromodomain Y-like protein Neighboring gene NANOG hESC enhancer GRCh37_chr3:16738083-16738584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16739803-16740450 Neighboring gene CDYL pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:16791041-16791542 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16810328-16810902 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:16830630-16831603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19555 Neighboring gene uncharacterized LOC105376972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16924592-16925300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14120

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_077176.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    16659462..16659756
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    16660638..16660932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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