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LOC121045486 Sharpr-MPRA regulatory regions 9818 and 11773 [ Homo sapiens (human) ]

Gene ID: 121045486, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121045486
Gene description
Sharpr-MPRA regulatory regions 9818 and 11773
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. Two overlapping subregions were validated as functional enhancers 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 Activating DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). One subregion also displayed repressive activity by Sharpr-MRPA in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC121045486 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (128068186..128068500)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (130802761..130803075)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (127787029..127787343)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene kelch repeat and BTB domain containing 12 Neighboring gene RNA, 5S ribosomal pseudogene 139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:127730388-127730888 Neighboring gene uncharacterized LOC102723759 Neighboring gene Sharpr-MPRA regulatory region 3038 Neighboring gene CRISPRi-FlowFISH-validated RPN1 regulatory element 1 Neighboring gene SEC61 translocon subunit alpha 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14701 Neighboring gene RUVBL1 antisense RNA 1 Neighboring gene RuvB like AAA ATPase 1 Neighboring gene RNA, U2 small nuclear 37, pseudogene

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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 11773
  • Sharpr-MPRA regulatory region 9818

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_074078.1 

    Range
    101..415
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    128068186..128068500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    130802761..130803075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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