U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC112577548 Sharpr-MPRA regulatory region 4759 [ Homo sapiens (human) ]

Gene ID: 112577548, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC112577548
Gene description
Sharpr-MPRA regulatory region 4759
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (228500904..228501262)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (227689404..227689762)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (228688669..228688963)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H2B clustered histone 27, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:228658552-228659062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:228663712-228664547 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:228673961-228674822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:228674823-228675683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:228675801-228676529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:228676530-228677257 Neighboring gene Sharpr-MPRA regulatory region 4602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:228680575-228681520 Neighboring gene ring finger protein 187 Neighboring gene uncharacterized LOC105373124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:228698839-228699340 Neighboring gene butyrophilin like 10, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:228736353-228737022 Neighboring gene RNA, 5S ribosomal pseudogene 19

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 2697
  • ATAC-STARR-seq lymphoblastoid silent region 1923

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_060468.2 

    Range
    101..459
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    228500904..228501262
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654708.1 Reference GRCh38.p14 PATCHES

    Range
    92103..92461
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    227689404..227689762
    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