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LOC107988032 Xq28 proximal FLNA-EMD recombination region [ Homo sapiens (human) ]

Gene ID: 107988032, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107988032
Gene description
Xq28 proximal FLNA-EMD recombination region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
misc_recomb: meiotic, non_allelic_homologous
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region is known to undergo non-allelic homologous recombination (NAHR) with a similar low-copy repeat region, the Xq28 distal FLNA-EMD recombination region, which is in reverse orientation relative to this region, and is located downstream of this region relative to the reference genome. NAHR between the repeat regions found in these recombination regions can lead to an inversion of the 48 kb intervening sequence, including the filamin A (FLNA) gene and the emerin (EMD) gene. This inversion is observed in about 20% of X chromosomes. While there is no phenotype associated with the inversion, recombination between sequences found within the inverted region has been found in some cases of Emery-Dreifuss muscular dystrophy (EDMD), resulting in a deletion of the EMD gene. There is a meiotic recombination hotspot that partially overlaps the low-copy inverted repeat. [provided by RefSeq, Jun 2016]
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Genomic context

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See LOC107988032 in Genome Data Viewer
Location:
Xq28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154335912..154349572)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152572427..152586105)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153564262..153577940)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene transketolase like 1 Neighboring gene uncharacterized LOC105373386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30057 Neighboring gene filamin A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153596747-153597274 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153597275-153597800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21087 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153599383-153599908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153599914-153600555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21098 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153608033-153608612 Neighboring gene Xq28 distal FLNA-EMD recombination region Neighboring gene uncharacterized LOC124905228 Neighboring gene emerin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21099 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21100 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153626083-153626628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30060 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153627173-153627718 Neighboring gene ribosomal protein L10

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. Human Xq28 inversion polymorphism: From sex linkage to Genomics--A genetic mother lode. Kirby CS, et al. Biochem Mol Biol Educ, 2016 Mar-Apr. PMID 26956943
  2. A recurrent inversion on the eutherian X chromosome. Cáceres M, et al. Proc Natl Acad Sci U S A, 2007 Nov 20. PMID 18003915, Free PMC Article
  3. Emerin deletions occurring on both Xq28 inversion backgrounds. Small K, et al. Hum Mol Genet, 1998 Jan. PMID 9384614
  4. Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats. Small K, et al. Nat Genet, 1997 May. PMID 9140403
  5. DNA recombination. Recombination initiation maps of individual human genomes. Pratto F, et al. Science, 2014 Nov 14. PMID 25395542, 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_050800.1 

    Range
    101..13761
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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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    154335912..154349572
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152572427..152586105
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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