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LOC123744830 Sharpr-MPRA regulatory region 11401 [ Homo sapiens (human) ]

Gene ID: 123744830, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123744830
Gene description
Sharpr-MPRA regulatory region 11401
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (56851791..56852085)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (56693405..56693699)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (56716589..56716883)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene collagen type XXI alpha 1 chain Neighboring gene NANOG hESC enhancer GRCh37_chr6:56142823-56143330 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56144052-56144553 Neighboring gene dihydrofolate reductase pseudogene 6 Neighboring gene regulator of chromosome condensation 2 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56399527-56400028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56400029-56400528 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:56406989-56407754 Neighboring gene MPRA-validated peak5860 silencer Neighboring gene dystonin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24703 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:56579434-56579994 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:56579995-56580556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56581759-56582299 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56616684-56617267 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17296 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56624276-56624832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24704 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:56640200-56641045 Neighboring gene MPRA-validated peak5861 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:56707357-56708225 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:56708226-56709093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24705 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24706 Neighboring gene DST antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92363 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92364 Neighboring gene ribosomal protein L17 pseudogene 26 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24707 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:56803197-56804396 Neighboring gene RNA, U6 small nuclear 626, pseudogene

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_078130.1 

    Range
    101..395
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    56851791..56852085
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    56693405..56693699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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