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LOC124310614 Sharpr-MPRA regulatory region 9654 [ Homo sapiens (human) ]

Gene ID: 124310614, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310614
Gene description
Sharpr-MPRA regulatory region 9654
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124310614 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 (98770827..98771121)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (110942475..110942769)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (101533109..101533403)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene gamma-aminobutyric acid type B receptor subunit 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101372736-101373728 Neighboring gene septin 7 pseudogene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:101430118-101430303 Neighboring gene uncharacterized LOC124902228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101468843-101469414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101469986-101470556 Neighboring gene Sharpr-MPRA regulatory region 5777 Neighboring gene ankyrin repeat and sterile alpha motif domain containing 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20120 Neighboring gene H3K27ac hESC enhancers GRCh37_chr9:101558100-101558600 and GRCh37_chr9:101558601-101559101 Neighboring gene uncharacterized LOC124902229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20123 Neighboring gene Sharpr-MPRA regulatory region 15412 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 12

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_078896.1 

    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
    98770827..98771121
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    110942475..110942769
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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