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LOC123480928 Sharpr-MPRA regulatory region 9584 [ Homo sapiens (human) ]

Gene ID: 123480928, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123480928
Gene description
Sharpr-MPRA regulatory region 9584
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (127352234..127352528)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (130655242..130655536)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (128273389..128273683)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 48 pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:127692753-127693387 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73151 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73157 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73174 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:127771052-127772251 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73198 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73219 Neighboring gene MPRA-validated peak5104 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:127941473-127942018 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73301 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:127988930-127989494 Neighboring gene uncharacterized LOC102724210 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73347 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73368 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73373 Neighboring gene uncharacterized LOC107986312 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73387 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:128328664-128328924 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73515 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_73569 Neighboring gene Sharpr-MPRA regulatory region 5357 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:128525826-128526649 Neighboring gene uncharacterized LOC105377412 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:128553760-128554299 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:128576502-128577102 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:128577103-128577701 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:128607842-128609041 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:128629462-128630661 Neighboring gene inturned planar cell polarity 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_077622.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    127352234..127352528
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    130655242..130655536
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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