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LOC124188226 Sharpr-MPRA regulatory region 8664 [ Homo sapiens (human) ]

Gene ID: 124188226, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124188226
Gene description
Sharpr-MPRA regulatory region 8664
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, Feb 2022]
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Genomic context

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See LOC124188226 in Genome Data Viewer
Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (125446867..125447161)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (126580316..126580610)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (126459109..126459403)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase Neighboring gene Sharpr-MPRA regulatory region 6874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27909 Neighboring gene RNA, 7SL, cytoplasmic 329, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:126312861-126313361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27910 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:126346157-126346974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:126389339-126389905 Neighboring gene Sharpr-MPRA regulatory region 8491 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:126398994-126399684 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:126401291-126401791 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:126400790-126401290 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:126416953-126417640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:126417641-126418327 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:126427297-126428194 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:126428195-126429092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27913 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:126433597-126434098 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:126434099-126434598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27915 Neighboring gene MPRA-validated peak7163 silencer Neighboring gene tribbles pseudokinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:126513538-126514038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27917 Neighboring gene TRIB1 associated lncRNA Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:126525111-126526310 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:126533553-126534054 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:126544853-126545039 Neighboring gene long intergenic non-protein coding RNA 2964 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:126558198-126558636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:126569037-126569774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27927 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:126667345-126668544 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:126691873-126693072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27928 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:126745383-126745936 Neighboring gene uncharacterized LOC105375747

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_078702.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    125446867..125447161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    126580316..126580610
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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