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LOC121725149 Sharpr-MPRA regulatory region 12200 [ Homo sapiens (human) ]

Gene ID: 121725149, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725149
Gene description
Sharpr-MPRA regulatory region 12200
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 matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (72186158..72186452)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (72226135..72226429)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (72235309..72235603)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 877 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72136311-72137027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:72137028-72137745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20071 Neighboring gene CCDC137 pseudogene 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:72148884-72149724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:72184639-72185213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20072 Neighboring gene long intergenic non-protein coding RNA 870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20076 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:72226281-72226881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14526 Neighboring gene NANOG hESC enhancer GRCh37_chr3:72242807-72243499 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:72245432-72246000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72252370-72252906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:72252907-72253442 Neighboring gene uncharacterized LOC124909393 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:72291263-72291470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20081 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20082 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:72318159-72319358 Neighboring gene uncharacterized LOC105377158 Neighboring gene CRISPRi-validated cis-regulatory element chr3.2860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:72340695-72341195 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:72348604-72349803 Neighboring gene Sharpr-MPRA regulatory region 8765

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_075618.1 

    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
    72186158..72186452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    72226135..72226429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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