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LOC122128431 Sharpr-MPRA regulatory region 2699 [ Homo sapiens (human) ]

Gene ID: 122128431, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122128431
Gene description
Sharpr-MPRA regulatory region 2699
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 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153914713..153915007)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (153051970..153052264)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153887189..153887483)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904425 Neighboring gene GATA zinc finger domain containing 2B Neighboring gene adipose differentiation-related protein pseudogene Neighboring gene Sharpr-MPRA regulatory region 14566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:153877149-153877650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1755 Neighboring gene uncharacterized LOC101928059 Neighboring gene Sharpr-MPRA regulatory region 4321 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:153897582-153897755 Neighboring gene DENN domain containing 4B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153918384-153918884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1347 Neighboring gene CREB regulated transcription coactivator 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_076451.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    153914713..153915007
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    153051970..153052264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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