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LOC107048982 origin of replication upstream of FMR1 [ Homo sapiens (human) ]

Gene ID: 107048982, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107048982
Gene description
origin of replication upstream of FMR1
Gene type
biological region
Feature type(s)
rep_origin
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region contains an origin of DNA replication located greater than 50 kb upstream of the FMR1 (Fragile X messenger ribonucleoprotein 1) gene. A C vs T single nucleotide polymorphism in this sequence (rs45631657) influences activity of this origin, with the C allele associated with decreased origin activity. Loss of origin activity is associated with Fragile X trinucleotide repeat expansion resulting in Fragile X Syndrome. [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC107048982 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (147857585..147858536)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (146122193..146123144)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (146939103..146940054)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene SLIRP. pseudogene 1 Neighboring gene RNA, U6 small nuclear 382, pseudogene Neighboring gene uncharacterized LOC105373349 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:146965512-146965690 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:146980170-146980670 Neighboring gene origin of replication in 5' region of FMR1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21039 Neighboring gene FMR1 antisense RNA 1

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. Cis-acting DNA sequence at a replication origin promotes repeat expansion to fragile X full mutation. Gerhardt J, et al. J Cell Biol, 2014 Sep 1. PMID 25179629, Free PMC Article
  2. The DNA replication program is altered at the FMR1 locus in fragile X embryonic stem cells. Gerhardt J, et al. Mol Cell, 2014 Jan 9. PMID 24289922, 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_046346.1 

    Range
    101..1052
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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
    147857585..147858536
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    146122193..146123144
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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