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LOC123522802 Sharpr-MPRA regulatory region 4960 [ Homo sapiens (human) ]

Gene ID: 123522802, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123522802
Gene description
Sharpr-MPRA regulatory region 4960
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (139468444..139468738)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (139993505..139993799)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (138848029..138848323)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RNA, U5B small nuclear 4, pseudogene Neighboring gene endothelial cell surface expressed chemotaxis and apoptosis regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23233 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138840510-138841099 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138841100-138841688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138842278-138842865 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138852141-138852662 Neighboring gene small integral membrane protein 33 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138854227-138854748 Neighboring gene stimulator of interferon response cGAMP interactor 1 Neighboring gene Sharpr-MPRA regulatory region 11914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23235

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_077831.1 

    Range
    101..395
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    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    139468444..139468738
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021159996.1 Reference GRCh38.p14 PATCHES

    Range
    58239..58533
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    139993505..139993799
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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