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LOC122889071 Sharpr-MPRA regulatory region 12551 [ Homo sapiens (human) ]

Gene ID: 122889071, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122889071
Gene description
Sharpr-MPRA regulatory region 12551
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 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889071 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (40312638..40312932)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (40327686..40327980)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (40354129..40354423)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene EIF1B antisense RNA 1 Neighboring gene uncharacterized LOC124906228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14230 Neighboring gene eukaryotic translation initiation factor 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19715 Neighboring gene phosphoglycerate mutase 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14231 Neighboring gene ENTPD3, EIF1B and MYRIP antisense RNA 1 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:40459610-40459810

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_077205.1 

    Range
    101..395
    Download
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    40312638..40312932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    40327686..40327980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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