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LOC124625861 Sharpr-MPRA regulatory region 2909 [ Homo sapiens (human) ]

Gene ID: 124625861, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124625861
Gene description
Sharpr-MPRA regulatory region 2909
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124625861 in Genome Data Viewer
Location:
11q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (124766193..124766487)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (124794856..124795150)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (124636089..124636383)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:124621349-124621910 Neighboring gene Sharpr-MPRA regulatory region 10895 Neighboring gene V-set and immunoglobulin domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124631741-124632244 Neighboring gene endothelial cell adhesion molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4029 Neighboring gene ESAM antisense RNA 1 Neighboring gene Myb/SANT DNA binding domain containing 2 Neighboring gene NANOG hESC enhancer GRCh37_chr11:124663166-124663667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4031 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:124669881-124670488 Neighboring gene MSANTD2 antisense RNA 1 Neighboring gene E3 ubiquitin-protein ligase RNF181-like

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_079461.1 

    Range
    101..395
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    124766193..124766487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    124794856..124795150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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