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LOC122128472 Sharpr-MPRA regulatory region 4419 [ Homo sapiens (human) ]

Gene ID: 122128472, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122128472
Gene description
Sharpr-MPRA regulatory region 4419
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [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 (167869731..167870025)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (167221214..167221508)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (167838969..167839263)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:167688821-167689320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1535 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:167691547-167692047 Neighboring gene tRNA-Pro (anticodon AGG) 2-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167697263-167697762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2053 Neighboring gene myelin protein zero like 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:167739237-167739808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:167740743-167741244 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:167761820-167761968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1538 Neighboring gene adenylate cyclase 10 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:167830579-167831095 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:167831096-167831613 Neighboring gene DDB1 and CUL4 associated factor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:167882400-167883076 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:167883077-167883753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2055 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1541 Neighboring gene mitochondrial pyruvate carrier 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:167956130-167957329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2056 Neighboring gene microRNA 1255b-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_076492.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    167869731..167870025
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    167221214..167221508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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