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LOC121099707 Sharpr-MPRA regulatory region 3450 [ Homo sapiens (human) ]

Gene ID: 121099707, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121099707
Gene description
Sharpr-MPRA regulatory region 3450
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (142655744..142656038)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (143186985..143187279)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (142035309..142035603)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein S12 pseudogene 10 Neighboring gene FGF1 promoter D Neighboring gene small nucleolar RNA SNORA36 family Neighboring gene FGF1 promoter C Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:142024170-142025369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142039508-142040008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142040009-142040509 Neighboring gene fibroblast growth factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142047003-142047511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142047512-142048019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142049247-142049746 Neighboring gene NANOG hESC enhancer GRCh37_chr5:142052360-142052880 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:142064129-142064998 Neighboring gene FGF1 promoter B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16473 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142150581-142151416 Neighboring gene long intergenic non-protein coding RNA 1844 Neighboring gene NANOG hESC enhancer GRCh37_chr5:142176991-142177492 Neighboring gene Rho GTPase activating protein 26 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16477 Neighboring gene ARHGAP26 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142242364-142242980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142242981-142243597 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142243598-142244214 Neighboring gene Sharpr-MPRA regulatory region 7053

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 16472

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_074187.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    142655744..142656038
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    143186985..143187279
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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