U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC112872302 Sharpr-MPRA regulatory region 12201 [ Homo sapiens (human) ]

Gene ID: 112872302, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC112872302
Gene description
Sharpr-MPRA regulatory region 12201
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 3:PromF, promoter flanking) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2018]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129614926..129615220)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132359364..132359658)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (129333769..129334063)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129261557-129262058 Neighboring gene Sharpr-MPRA regulatory region 2951 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129277154-129278043 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129291899-129292624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129295530-129296256 Neighboring gene H1.8 linker histone Neighboring gene plexin D1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129315061-129315792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129321778-129322770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129323763-129324755 Neighboring gene RNA, 7SL, cytoplasmic 752, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129325748-129326740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129326741-129327731 Neighboring gene uncharacterized LOC124909431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129330613-129331535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129331536-129332457 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129342361-129343136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129343789-129344398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20518 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:129358807-129359416 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:129360029-129360638 Neighboring gene CARMIL2 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 9069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129376963-129377790 Neighboring gene transmembrane and coiled-coil domain family 1 Neighboring gene Sharpr-MPRA regulatory region 11052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129409826-129410443 Neighboring gene NANOG hESC enhancer GRCh37_chr3:129414696-129415307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129453832-129454332 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:129513146-129514345 Neighboring gene RNY3 pseudogene 13

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_061361.1 

    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
    129614926..129615220
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    132359364..132359658
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases