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LOC124433255 Sharpr-MPRA regulatory region 9650 [ Homo sapiens (human) ]

Gene ID: 124433255, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124433255
Gene description
Sharpr-MPRA regulatory region 9650
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (46541959..46542253)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (46698013..46698307)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (46563509..46563803)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene autophagy and beclin 1 regulator 1 Neighboring gene ribosomal protein S10 pseudogene 19 Neighboring gene NANOG hESC enhancer GRCh37_chr11:46467611-46468112 Neighboring gene microRNA 3160-1 Neighboring gene microRNA 3160-2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3313 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:46559175-46559678 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46559679-46560184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:46587793-46588293 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4681 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:46605824-46606668 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:46615325-46615825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4683 Neighboring gene Sharpr-MPRA regulatory region 32 Neighboring gene harbinger transposase derived 1 Neighboring gene autophagy related 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:46715957-46716456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3314 Neighboring gene Rho GTPase activating protein 1

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_079276.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    46541959..46542253
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    46698013..46698307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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