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LOC122128445 Sharpr-MPRA regulatory region 3040 [ Homo sapiens (human) ]

Gene ID: 122128445, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122128445
Gene description
Sharpr-MPRA regulatory region 3040
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jul 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 (156247918..156248212)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155386375..155386669)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156217709..156218003)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1856 Neighboring gene PMF1-BGLAP readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1422 Neighboring gene polyamine modulated factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1857 Neighboring gene BGLAP promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1424 Neighboring gene bone gamma-carboxyglutamate protein Neighboring gene progestin and adipoQ receptor family member 6 Neighboring gene SMG5 nonsense mediated mRNA decay factor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156250697-156251670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1425 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:156252643-156253614 Neighboring gene transmembrane protein 79 Neighboring gene Sharpr-MPRA regulatory regions 9834 and 13552 Neighboring gene glycosylated lysosomal membrane protein

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_076465.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    156247918..156248212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    155386375..155386669
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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