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LOC123864076 Sharpr-MPRA regulatory region 12163 [ Homo sapiens (human) ]

Gene ID: 123864076, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123864076
Gene description
Sharpr-MPRA regulatory region 12163
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123864076 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (136426511..136426805)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (137614673..137614967)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (136747649..136747943)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene microtubule associated protein 7 Neighboring gene ribosomal protein lateral stalk subunit P1 pseudogene 8 Neighboring gene MPRA-validated peak6144 silencer Neighboring gene phosphopantothenate--cysteine ligase-like Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90180 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90214 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90217 Neighboring gene MPRA-validated peak6145 silencer Neighboring gene NADH:ubiquinone oxidoreductase subunit S5 pseudogene 1 Neighboring gene MPRA-validated peak6146 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:136846904-136847714 Neighboring gene RN7SK pseudogene 299

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_078208.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    136426511..136426805
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    137614673..137614967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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