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LOC123775391 Sharpr-MPRA regulatory region 3240 [ Homo sapiens (human) ]

Gene ID: 123775391, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123775391
Gene description
Sharpr-MPRA regulatory region 3240
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123775391 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (100482733..100483027)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (101656482..101656776)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (100930609..100930903)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene arginase 2 pseudogene Neighboring gene VISTA enhancer hs576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17424 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:100729120-100729639 Neighboring gene Sharpr-MPRA regulatory region 11257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:100802848-100803481 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:100893988-100894670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:100895353-100896034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:100896035-100896716 Neighboring gene SIM1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:100902959-100903520 Neighboring gene VISTA enhancer hs2319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:100905055-100906036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:100915529-100916120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24866 Neighboring gene SIM bHLH transcription factor 1 Neighboring gene defective in cullin neddylation 1 domain containing 1 pseudogene Neighboring gene activating signal cointegrator 1 complex subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24867 Neighboring gene uncharacterized LOC107984041 Neighboring gene mitogen-activated protein kinase 1 interacting protein 1 like 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_078159.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    100482733..100483027
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    101656482..101656776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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