U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123620115 Sharpr-MPRA regulatory region 8968 [ Homo sapiens (human) ]

Gene ID: 123620115, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123620115
Gene description
Sharpr-MPRA regulatory region 8968
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Dec 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC123620115 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41455851..41456145)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41284867..41285161)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41423589..41423883)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100505711 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41374298-41375106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41375914-41376721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41376722-41377528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41396875-41397374 Neighboring gene uncharacterized LOC107986538 Neighboring gene VISTA enhancer hs2104 Neighboring gene uncharacterized LOC112267957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41424325-41425112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41438012-41438663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41459644-41460288 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:41461668-41461828 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41470387-41471134 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41471135-41471882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41473163-41473662 Neighboring gene long intergenic non-protein coding RNA 1276 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr6:41499390-41499960 and GRCh37_chr6:41499961-41500529 Neighboring gene FOXP4 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 11601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24511 Neighboring gene Sharpr-MPRA regulatory region 4049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17186 Neighboring gene forkhead box P4

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_078099.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    41455851..41456145
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    41284867..41285161
    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