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LOC124433253 Sharpr-MPRA regulatory region 31 [ Homo sapiens (human) ]

Gene ID: 124433253, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124433253
Gene description
Sharpr-MPRA regulatory region 31
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive and primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 4:PromP). [provided by RefSeq, Jan 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 (45898890..45899692)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (46054820..46055622)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45920949..45921243)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4666 Neighboring gene solute carrier family 35 member C1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4669 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45869217-45869738 Neighboring gene Sharpr-MPRA regulatory region 9087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4671 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:45880664-45881863 Neighboring gene cryptochrome circadian regulator 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:45882374-45883573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45887051-45887552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3290 Neighboring gene mitogen-activated protein kinase 8 interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45917073-45917944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45917945-45918814 Neighboring gene uncharacterized LOC124902668 Neighboring gene Sharpr-MPRA regulatory region 10000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45927125-45927626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45927627-45928126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45929145-45930090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45938484-45939236 Neighboring gene Frey regulator of sperm-oocyte fusion 1 Neighboring gene peroxisomal biogenesis factor 16

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K4me1 hESC enhancer GRCh37_chr11:45920441-45921110

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_079274.2 

    Range
    101..903
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    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
    45898890..45899692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    46054820..46055622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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