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LOC112935907 Sharpr-MPRA regulatory region 12227 [ Homo sapiens (human) ]

Gene ID: 112935907, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112935907
Gene description
Sharpr-MPRA regulatory region 12227
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, Aug 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 (171159140..171159434)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (173943459..173943753)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (170876929..170877223)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 2 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14889 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:170779459-170780037 Neighboring gene MPRA-validated peak4922 silencer Neighboring gene uncharacterized LOC105374216 Neighboring gene TRAF2 and NCK interacting kinase Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:170834472-170835140 Neighboring gene microRNA 569 Neighboring gene Sharpr-MPRA regulatory region 1564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14890 Neighboring gene NANOG hESC enhancer GRCh37_chr3:170904542-170905069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20808 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:170924049-170924658 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:170952794-170952983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20813 Neighboring gene VISTA enhancer hs2120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20814 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:171101812-171102358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20815 Neighboring gene uncharacterized LOC124906303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14893 Neighboring gene uncharacterized LOC102724479 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:171178895-171179395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14894

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_061424.1 

    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
    171159140..171159434
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    173943459..173943753
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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