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LOC123956226 Sharpr-MPRA regulatory region 5703 [ Homo sapiens (human) ]

Gene ID: 123956226, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123956226
Gene description
Sharpr-MPRA regulatory region 5703
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 DNase matched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956226 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (132965469..132965763)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (134286986..134287280)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (132650229..132650523)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD46 Neighboring gene uncharacterized LOC100506937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:132443779-132444332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:132455865-132456366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:132456367-132456866 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:132558086-132558347 Neighboring gene Sharpr-MPRA regulatory region 15449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26681 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:132728273-132728435 Neighboring gene eukaryotic translation elongation factor 1 gamma pseudogene Neighboring gene microRNA 3654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:132766583-132767217 Neighboring gene RNA, U6 small nuclear 92, 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_078420.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    132965469..132965763
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    134286986..134287280
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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