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LOC112872300 Sharpr-MPRA regulatory region 8693 [ Homo sapiens (human) ]

Gene ID: 112872300, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112872300
Gene description
Sharpr-MPRA regulatory region 8693
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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 23:Low, low signal proximal to active elements), with weak activation in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jul 2018]
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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 (129448346..129448640)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132193183..132193477)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (129167189..129167483)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129129626-129130126 Neighboring gene EF-hand calcium binding domain 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129137243-129137742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20517 Neighboring gene methyl-CpG binding domain 4, DNA glycosylase Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:129168229-129168945 Neighboring gene intraflagellar transport 122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129200162-129201039 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:129208521-129208729 Neighboring gene Sharpr-MPRA regulatory region 10640 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:129213542-129214741 Neighboring gene MPRA-validated peak4826 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129247433-129248158 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129248159-129248884 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:129253999-129254668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129261557-129262058 Neighboring gene rhodopsin enhancer region Neighboring gene Sharpr-MPRA regulatory region 2951 Neighboring gene rhodopsin Neighboring gene H1.8 linker histone

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_061359.1 

    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
    129448346..129448640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    132193183..132193477
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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