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LOC121099721 Sharpr-MPRA regulatory region 9692 [ Homo sapiens (human) ]

Gene ID: 121099721, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121099721
Gene description
Sharpr-MPRA regulatory region 9692
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 25:Art, potential CNV or repetitive artifacts), with weaker activity in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Apr 2021]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (4125955..4126249)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (3995243..3995537)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (4126189..4126483)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23896 Neighboring gene pre-mRNA processing factor kinase PRP4K Neighboring gene Sharpr-MPRA regulatory region 2502 Neighboring gene uncharacterized LOC124901553 Neighboring gene family with sequence similarity 217 member A Neighboring gene testis expressed 56, pseudogene Neighboring gene enoyl-CoA delta isomerase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16860 Neighboring gene uncharacterized LOC107986559 Neighboring gene uncharacterized LOC124901246 Neighboring gene ECI2 divergent transcript Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:4168819-4169425 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:4169426-4170031 Neighboring gene CRISPRi-validated cis-regulatory element chr6.285

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_074201.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    4125955..4126249
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    3995243..3995537
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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