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LOC121331339 Sharpr-MPRA regulatory region 12902 [ Homo sapiens (human) ]

Gene ID: 121331339, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121331339
Gene description
Sharpr-MPRA regulatory region 12902
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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121331339 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (99167147..99167441)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (111338859..111339153)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (101929429..101929723)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene collagen type XV alpha 1 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101724037-101724537 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:101725038-101725622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101733335-101733912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101733913-101734490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101760575-101761331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101761332-101762087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101834020-101834520 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101834521-101835021 Neighboring gene CRISPRi-validated cis-regulatory element chr9.1735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20125 Neighboring gene transforming growth factor beta receptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28699 Neighboring gene RNA, 5S ribosomal pseudogene 290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101932965-101933747 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103896 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101941126-101941626 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101941627-101942127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28700 Neighboring gene uncharacterized LOC105376174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28701 Neighboring gene RNA, 7SL, cytoplasmic 794, 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)

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_074363.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    99167147..99167441
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    111338859..111339153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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