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LOC108491837 IGL region enhancer-blocking element 22-2 [ Homo sapiens (human) ]

Gene ID: 108491837, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108491837
Gene description
IGL region enhancer-blocking element 22-2
Gene type
biological region
Feature type(s)
regulatory: enhancer, enhancer_blocking_element
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region is located in the immunoglobulin lambda locus (IGL) of chromosome 22, and it overlaps the 5' ends of both the PRAME (preferentially expressed antigen in melanoma) and opposite strand LOC648691 (uncharacterized non-protein-coding) genes. A sub-region was identified as a putative enhancer-blocking chromatin insulator based on strong CTCF association by ChIP-seq analysis in K562 erythroleukemia cells. It was validated as a functional enhancer-blocking element based on its ability to block activity of an erythroid enhancer when positioned between the enhancer and a promoter in a lentiviral reporter assay in K562 erythroleukemia cells. In addition, an overlapping sub-region 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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
22q11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (22559162..22559476)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (22982022..22982336)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (22901569..22901883)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene immunoglobulin lambda locus Neighboring gene uncharacterized LOC124905161 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:22874253-22875452 Neighboring gene uncharacterized LOC648691 Neighboring gene zinc finger protein 280B Neighboring gene ReSE screen-validated silencer GRCh37_chr22:22896585-22896782 Neighboring gene NANOG hESC enhancer GRCh37_chr22:22915922-22916455 Neighboring gene zinc finger protein 280A Neighboring gene Sharpr-MPRA regulatory region 7390 Neighboring gene immunoglobulin lambda variable 2-34 (pseudogene) Neighboring gene PRAME nuclear receptor transcriptional regulator Neighboring gene immunoglobulin lambda variable 2-33 (non-functional)

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. Identification and characterization of enhancer-blocking insulators to reduce retroviral vector genotoxicity. Groth AC, et al. PLoS One, 2013. PMID 24098520, Free PMC Article
  2. Widespread plasticity in CTCF occupancy linked to DNA methylation. Wang H, et al. Genome Res, 2012 Sep. PMID 22955980, Free PMC Article
  3. 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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 1631
  • chromatin insulator 22-2

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_051352.2 

    Range
    101..415
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    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    22559162..22559476
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187629.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    194819..195133
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    22982022..22982336
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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