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LOC124946345 Sharpr-MPRA regulatory region 43 [ Homo sapiens (human) ]

Gene ID: 124946345, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124946345
Gene description
Sharpr-MPRA regulatory region 43
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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 1:Tss). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
13q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (113363714..113364008)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (112617914..112618208)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (114018029..114018323)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene growth hormone regulated TBC protein 1 Neighboring gene MAGE-like protein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:114003074-114003239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114003888-114004548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114004549-114005209 Neighboring gene GRTP1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114019311-114020004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114020005-114020698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114021393-114022086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114027480-114028460 Neighboring gene uncharacterized LOC124903218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114032969-114033953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114047778-114048319 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5546 Neighboring gene Sharpr-MPRA regulatory region 10007 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114059695-114060489 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114061607-114062292 Neighboring gene ADP-ribosylhydrolase like 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:114064726-114065925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114071164-114072164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114072165-114073165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114075358-114076070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114076783-114077494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114080191-114080738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114085068-114085648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114100205-114101146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114105835-114106336

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_080051.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    113363714..113364008
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    112617914..112618208
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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