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LOC123864083 Sharpr-MPRA regulatory region 8989 [ Homo sapiens (human) ]

Gene ID: 123864083, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123864083
Gene description
Sharpr-MPRA regulatory region 8989
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, Jan 2022]
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Genomic context

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See LOC123864083 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 (139376752..139377046)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (140560654..140560948)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (139697889..139698183)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene DnaJ heat shock protein family (Hsp40) member C7 pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:139689956-139690774 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17611 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17612 Neighboring gene Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2 Neighboring gene uncharacterized LOC107986651 Neighboring gene CRISPRi-validated cis-regulatory element chr6.4959 Neighboring gene CRISPRi-validated cis-regulatory element chr6.4960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:139794122-139794622 Neighboring gene long intergenic non-protein coding RNA 1625

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_078215.1 

    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
    139376752..139377046
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    140560654..140560948
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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