U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC112935919 Sharpr-MPRA regulatory region 14389 [ Homo sapiens (human) ]

Gene ID: 112935919, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC112935919
Gene description
Sharpr-MPRA regulatory region 14389
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 K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone), with weaker activity in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [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
See LOC112935919 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (190386420..190386714)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (193202792..193203086)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (190104209..190104503)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:189894452-189894952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:189894953-189895453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20985 Neighboring gene NMNAT1 pseudogene 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:189949260-189950459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15001 Neighboring gene claudin 16 Neighboring gene claudin 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:190080003-190080564 Neighboring gene Sharpr-MPRA regulatory region 3521 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:190158638-190158813 Neighboring gene transmembrane protein 207 Neighboring gene Sharpr-MPRA regulatory region 15127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:190232063-190232564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:190232565-190233064 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:190258615-190259497 Neighboring gene interleukin 1 receptor accessory protein Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:190283646-190284845 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:190302729-190303262 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:190303263-190303796 Neighboring gene glucosaminyl (N-acetyl) transferase 1 pseudogene 3

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_061434.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    190386420..190386714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    193202792..193203086
    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