U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC124849289 Sharpr-MPRA regulatory region 9670 [ Homo sapiens (human) ]

Gene ID: 124849289, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC124849289
Gene description
Sharpr-MPRA regulatory region 9670
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element 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 Repressive non-DNase unmatched - State 17:Gen3', transcription 3' end of genes, highly expressed, more exonic) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Mar 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC124849289 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (131944604..131944898)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (131992654..131992948)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5102 Neighboring gene Sharpr-MPRA regulatory region 8404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132381351-132382148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132384711-132385228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132385229-132385746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132385901-132386674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132386675-132387447 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25936 Neighboring gene unc-51 like autophagy activating kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7373 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:132409300-132410176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5107 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25941 Neighboring gene PUS1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5109 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132434951-132435658 Neighboring gene Sharpr-MPRA regulatory region 13568 Neighboring gene pseudouridine synthase 1 Neighboring gene E1A binding protein p400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132470576-132471195 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132471868-132472518 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132473169-132473818 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:132490339-132491538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132498351-132499144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132499145-132499938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132499948-132500448 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:132508440-132509639 Neighboring gene Sharpr-MPRA regulatory region 9648 Neighboring gene small nucleolar RNA, H/ACA box 49 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132534021-132534992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132567429-132567930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132569347-132570207 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:132570983-132571159 Neighboring gene EP400 pseudogene 1 Neighboring gene uncharacterized LOC107987169

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

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_079864.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    131944604..131944898
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    131992654..131992948
    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