U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123477730 Sharpr-MPRA regulatory region 4409 [ Homo sapiens (human) ]

Gene ID: 123477730, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123477730
Gene description
Sharpr-MPRA regulatory region 4409
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Nov 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC123477730 in Genome Data Viewer
Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (39970789..39971083)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (39940750..39941046)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (39972409..39972703)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 K Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:39787697-39788198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:39788199-39788698 Neighboring gene zinc finger and BTB domain containing 12B, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:39821819-39822356 Neighboring gene PDS5 cohesin associated factor A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21469 Neighboring gene RNA, 5S ribosomal pseudogene 159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21470 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:39977870-39978778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:39991585-39992282 Neighboring gene poly(A) binding protein cytoplasmic 1 pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:40000455-40000959 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40001597-40002110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40002111-40002626 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40002627-40003140 Neighboring gene keratin 18 pseudogene 25

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_077533.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    39970789..39971083
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    39940750..39941046
    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