Selected-GenAtlas references SOURCE GeneCards NCBI Gene Orphanet Ensembl
HGNC UniGene Nucleotide OMIM UCSC
Home Page
FLASH GENE
Symbol KCNQ1OT1 contributors: mct - updated : 26-04-2017
HGNC name KCNQ1 overlapping transcript 1 (non-protein coding)
HGNC id 6295
Corresponding disease
BWS Beckwith-Wiedemann syndrome
IH isolated body asymmetry
Location 11p15.5      Physical location : 2.661.767 - 2.721.228
Synonym name
  • KCNQ1 overlapping transcript 1
  • long QT intronic transcript 1
  • overlaping with the differentially methylated imprinting center for domain 2
  • non-protein coding RNA 12
  • Synonym symbol(s) LIT1, KvDMR1, KvLQT1-AS, DMR2, ICR21, NCRNA00012, FLJ41078
    DNA
    TYPE chromosome region
    SPECIAL FEATURE gene in gene, antisens
    text intronic transcript 1, embedded in intron 9 (and 10) of KCNQ1, in opposite orientation
    regulatory sequence Promoter (CAAT box)
    cytosine-phosphate-guanine/HTF
    Binding site   silencer
    text structure
  • intronic CpG-promoter and 5' end differentially methylated
  • silencer sequence in the promoter
  • promoter is approximately 300 bp and surrounded by inhibitory elements within the CpG island.
  • four CCAAT boxes upstream of the 5'-most start site regulating activity of the promoter and genomic imprinting
  • CTNNB1 can promote KCNQ1OT1 transcription through direct binding to the KCNQ1OT1 promoter
  • MAPPING cloned Y linked N status confirmed
    Map pter - TNNT3 - H19 - IGF2 - INS - TH - ASCL2 - TSPAN32 - CD81 - TSSC4 - TRPM5 - KCNQ1OT1 - KCNQ1 - C11orf21 - CDKN1C - SLC22A18 - PHLDA2 - NAP1L4 - CARS - cen
    RNA
    TRANSCRIPTS type untranslated
    text containing regulatory elements playing a mechanistic role in the BWS phenotype when paternally inherited
    EXPRESSION
    Rna function KCNQ1OT1 RNA interacts with chromatin through its most 5prime 20 kb sequence, providing a mechanism likely mediating the silencing activity of this long non-coding RNA
    Type
       expressed in (based on citations)
    organ(s)
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    IMPRINTING maternally
    text expressed in most tissues from the paternal allele, the maternal allele being imprinted through a specific methylation of a conserved CpG island
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • N-terminal silencing domain also required to target the episomal vector to the perinucleolar compartment during mid-S phase
  • HOMOLOGY
    Homologene
    FAMILY
    CATEGORY
    SUBCELLULAR LOCALIZATION
    basic FUNCTION
  • differentially methylated in oocytes at different stages of their development: germinal vesicle (GV), metaphase I (MI) or metaphase II (MII) (about 60 p100 of alleles were fully methylated in GV oocytes and full imprint is acquired in most MII oocytes)
  • implicated in long-range bidirectional silencing
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling
    a component
    INTERACTION
    DNA
    RNA
    small molecule
    protein
  • in later developmental stages, KCNQ1OT1 has a role in modulating KCNQ1 levels, since its absence leads to overexpression of KCNQ1
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) BWS , IH
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    constitutional     --other  
    hypo or hypermethylation incomplete in BWS patients, not associated with increased tumor risk (but increased frequence of midline abdominal-wall defects and macrosomia)
    constitutional   LOI    
    5' end hypomethylation in familial or sporadic cases of BWS (disturbing imprinting switch mechanism) and in liver, breast, cervical and gastric carcinoma
    constitutional   LOI    
    through factors interfering with normal oocyte differentiation such as gonadotrophin stimulation and in vitro maturation (IVM) (may possibly alter imprint resetting)
    constitutional       gain of function
    loss of methylation on the maternal allele correlated with loss of histone H3 lysine 9 methylation in BWS (50 percent of the cases)
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS