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LOC123575639 Sharpr-MPRA regulatory region 9005 [ Homo sapiens (human) ]

Gene ID: 123575639, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575639
Gene description
Sharpr-MPRA regulatory region 9005
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 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123575639 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (180844489..180844783)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (181400825..181401119)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (180271489..180271783)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:180212035-180212946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:180212947-180213857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:180224505-180225006 Neighboring gene alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr5:180229118-180229825 and GRCh37_chr5:180229826-180230532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:180231240-180231945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16773 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23771 Neighboring gene Sharpr-MPRA regulatory region 14850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16777 Neighboring gene long intergenic non-protein coding RNA 847 Neighboring gene ZFP62 zinc finger protein Neighboring gene hepatocellular carcinoma up-regulated EZH2-associated long non-coding RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:180288413-180289319 Neighboring gene uncharacterized LOC124901155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23773 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:180334710-180335266 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:180335267-180335821 Neighboring gene butyrophilin like 8 Neighboring gene ribosomal protein S29 pseudogene 12

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_077898.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    180844489..180844783
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    181400825..181401119
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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