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LOC122889047 Sharpr-MPRA regulatory region 9690 [ Homo sapiens (human) ]

Gene ID: 122889047, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889047
Gene description
Sharpr-MPRA regulatory region 9690
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889047 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 (17449757..17450051)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (17451941..17452235)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (17491249..17491543)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene phospholipase C like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19562 Neighboring gene PLCL2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19563 Neighboring gene Sharpr-MPRA regulatory region 1226 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_66731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:17192997-17193498 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:17194853-17195024 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:17199910-17200410 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:17200411-17200911 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:17211116-17211616 Neighboring gene NANOG hESC enhancer GRCh37_chr3:17217563-17218064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19568 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14124 Neighboring gene TBC1 domain family member 5 Neighboring gene Sharpr-MPRA regulatory region 10783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19570 Neighboring gene MPRA-validated peak4551 silencer Neighboring gene RBIS pseudogene 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:17535720-17536296 Neighboring gene ribosomal protein L31 pseudogene 19 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:17588257-17589120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19571 Neighboring gene MPRA-validated peak4555 silencer Neighboring gene RNA, U7 small nuclear 10 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_077179.1 

    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
    17449757..17450051
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    17451941..17452235
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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