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LOC124433254 Sharpr-MPRA regulatory region 2210 [ Homo sapiens (human) ]

Gene ID: 124433254, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124433254
Gene description
Sharpr-MPRA regulatory region 2210
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. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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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 (46382334..46382653)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (46538410..46538729)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (46403909..46404203)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46312695-46313398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3301 Neighboring gene cAMP responsive element binding protein 3 like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:46328063-46328758 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:46352624-46352765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46357769-46358498 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46360689-46361418 Neighboring gene Sharpr-MPRA regulatory region 11965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3303 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:46369312-46369525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46369839-46370824 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46373336-46374190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46374191-46375045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46375046-46375899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46377222-46378090 Neighboring gene diacylglycerol kinase zeta Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:46390736-46391935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46401950-46402584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46411613-46412218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46412219-46412822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3311 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46414340-46415114 Neighboring gene microRNA 4688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46428977-46429764 Neighboring gene cholinergic receptor muscarinic 4 Neighboring gene midkine Neighboring gene autophagy and beclin 1 regulator 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:46448914-46449505 Neighboring gene ribosomal protein S10 pseudogene 19

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 3308

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_079275.2 

    Range
    101..420
    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
    46382334..46382653
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    46538410..46538729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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