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LOC122094872 Sharpr-MPRA regulatory region 13550 [ Homo sapiens (human) ]

Gene ID: 122094872, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122094872
Gene description
Sharpr-MPRA regulatory region 13550
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (93552672..93552966)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (93398404..93398698)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (94018229..94018523)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene formin binding protein 1 like Neighboring gene RNA, 5S ribosomal pseudogene 53 Neighboring gene tRNA-Cys (anticodon GCA) 7-1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:94018571-94019099 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:94038039-94039036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:94050266-94050778 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94054146-94054690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94054691-94055235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:94057721-94058221 Neighboring gene BCAR3 adaptor protein, NSP family member Neighboring gene BCAR3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:94075253-94075816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94079051-94079704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94079705-94080357 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94081011-94081663 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94082971-94083623 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94101848-94102406 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:94102407-94102965 Neighboring gene Sharpr-MPRA regulatory region 755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94104972-94105607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1333 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94109607-94110328 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:94127441-94128640 Neighboring gene Sharpr-MPRA regulatory region 8830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1084 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:94158555-94159754 Neighboring gene uncharacterized LOC102723480 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:94166702-94167901

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_076386.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    93552672..93552966
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    93398404..93398698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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