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LOC112042779 Sharpr-MPRA regulatory region 11099 [ Homo sapiens (human) ]

Gene ID: 112042779, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112042779
Gene description
Sharpr-MPRA regulatory region 11099
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Feb 2018]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119191300..119191594)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119211670..119211964)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (119062009..119062303)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NHERF family PDZ scaffold protein 4 Neighboring gene small nucleolar RNA, C/D box 150 Neighboring gene dynein regulatory complex subunit 12 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3976 Neighboring gene fragile site, folic acid type, rare, fra(11)(q23.3) Neighboring gene Cbl proto-oncogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5628 Neighboring gene RNA, U6 small nuclear 262, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119177198-119177943 Neighboring gene microRNA 6756 Neighboring gene melanoma cell adhesion molecule

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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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_056428.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    119191300..119191594
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    119211670..119211964
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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