U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121627969 Sharpr-MPRA regulatory region 5152 [ Homo sapiens (human) ]

Gene ID: 121627969, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121627969
Gene description
Sharpr-MPRA regulatory region 5152
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jun 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (47577450..47577744)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46987340..46987634)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (47436849..47437143)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905183 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:47372169-47372670 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:47372671-47373170 Neighboring gene MPRA-validated peak7378 silencer Neighboring gene NUS1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20806 Neighboring gene Sharpr-MPRA regulatory region 9461 Neighboring gene uncharacterized LOC124905184 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:47415445-47415946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20807 Neighboring gene Sharpr-MPRA regulatory region 4668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:47434199-47434706 Neighboring gene A-Raf proto-oncogene, serine/threonine kinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:47434707-47435213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:47435306-47435806 Neighboring gene CRISPRi-FlowFISH-validated HDAC6 regulatory element 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20809 Neighboring gene synapsin I Neighboring gene Sharpr-MPRA regulatory region 5754 Neighboring gene TIMP metallopeptidase inhibitor 1 Neighboring gene microRNA 4769

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_075449.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    47577450..47577744
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    46987340..46987634
    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