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LOC123864073 Sharpr-MPRA regulatory region 12483 [ Homo sapiens (human) ]

Gene ID: 123864073, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123864073
Gene description
Sharpr-MPRA regulatory region 12483
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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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (135191791..135192085)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (136380035..136380329)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (135512929..135513223)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901405 Neighboring gene uncharacterized LOC124901406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25099 Neighboring gene uncharacterized LOC105378010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25100 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:135491500-135491716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17563 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25102 Neighboring gene uncharacterized LOC105378011 Neighboring gene MYB proto-oncogene, transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25104 Neighboring gene microRNA 548a-2

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_078205.1 

    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
    135191791..135192085
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    136380035..136380329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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