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LOC123466233 Sharpr-MPRA regulatory region 388 [ Homo sapiens (human) ]

Gene ID: 123466233, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123466233
Gene description
Sharpr-MPRA regulatory region 388
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123466233 in Genome Data Viewer
Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (10111585..10111879)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (10111163..10111457)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (10113209..10113503)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900665 Neighboring gene WD repeat domain 1 Neighboring gene microRNA 3138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:10092819-10093589 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:10095904-10096674 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:10097252-10098451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:10104010-10104700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:10104701-10105391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:10109091-10109822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:10114947-10115447 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:10117280-10118084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15278 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15279 Neighboring gene uncharacterized LOC124900666 Neighboring gene RNA, 5S ribosomal pseudogene 155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21311

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_077508.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    10111585..10111879
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    10111163..10111457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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