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LOC121832834 Sharpr-MPRA regulatory region 4123 [ Homo sapiens (human) ]

Gene ID: 121832834, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121832834
Gene description
Sharpr-MPRA regulatory region 4123
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer 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 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 4:PromP). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (48995466..48995760)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (48957641..48957935)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (49389249..49389543)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49378822-49379344 Neighboring gene Wnt family member 1 Neighboring gene uncharacterized LOC105369756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4421 Neighboring gene Sharpr-MPRA regulatory region 2140 Neighboring gene Sharpr-MPRA regulatory region 4008 Neighboring gene DDN and PRKAG1 antisense RNA 1 Neighboring gene dendrin Neighboring gene protein kinase AMP-activated non-catalytic subunit gamma 1 Neighboring gene Sharpr-MPRA regulatory region 4712 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49411600-49412190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6302 Neighboring gene lysine methyltransferase 2D Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:49442744-49443943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49443977-49444477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4422 Neighboring gene Sharpr-MPRA regulatory region 5975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6303

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_075909.1 

    Range
    101..395
    Download
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    48995466..48995760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    48957641..48957935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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