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LOC113939949 Sharpr-MPRA regulatory region 5546 [ Homo sapiens (human) ]

Gene ID: 113939949, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113939949
Gene description
Sharpr-MPRA regulatory region 5546
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO). [provided by RefSeq, Jan 2019]
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Genomic context

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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (15765912..15766206)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (15770848..15771142)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15859769..15860063)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene myosin heavy chain 11 Neighboring gene uncharacterized LOC124903650 Neighboring gene uncharacterized LOC124903651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15901002-15901817 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:15929109-15929286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15951931-15952432 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:15972689-15973888 Neighboring gene RNA, U6 small nuclear 213, pseudogene Neighboring gene centrosomal protein 20 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:15993095-15994294 Neighboring gene uncharacterized LOC107984869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:16018443-16018944 Neighboring gene ribosomal protein L15 pseudogene 20

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 duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. Loftus BJ, et al. Genomics, 1999 Sep 15. PMID 10493829
  2. 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_063734.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    15765912..15766206
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1423923..1424217
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    15770848..15771142
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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