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LOC121725161 Sharpr-MPRA regulatory region 6188 [ Homo sapiens (human) ]

Gene ID: 121725161, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725161
Gene description
Sharpr-MPRA regulatory region 6188
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (172182119..172182413)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (174967212..174967506)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (171899909..171900203)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:171678336-171678836 Neighboring gene FOXA motif-containing MPRA enhancer 130 Neighboring gene NANOG hESC enhancer GRCh37_chr3:171727625-171728138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20816 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:171757188-171757855 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:171757856-171758522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20817 Neighboring gene fibronectin type III domain containing 3B Neighboring gene HNF1 motif-containing MPRA enhancer 67 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20820 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:171854185-171855008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:171858305-171859128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20821 Neighboring gene Sharpr-MPRA regulatory region 1756 Neighboring gene uncharacterized LOC124906304 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:171884751-171885290 Neighboring gene Sharpr-MPRA regulatory region 4529 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:171911885-171912075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:171927153-171927716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:171927717-171928279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20825 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:171940563-171941066 Neighboring gene Sharpr-MPRA regulatory region 15581 Neighboring gene RPS27A pseudogene 8 Neighboring gene RNA, 7SL, cytoplasmic 141, pseudogene

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_075631.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    172182119..172182413
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    174967212..174967506
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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