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FLASH GENE
Symbol TCOF1 contributors: mct - updated : 05-01-2015
HGNC name Treacher Collins-Franceschetti syndrome 1
HGNC id 11654
DNA
TYPE functioning gene
STRUCTURE 42.67 kb     26 Exon(s)
10 Kb 5' upstream gene genomic sequence study
regulatory sequence Promoter
Binding site   transcription factor
motif repetitive sequence   other
text structure
  • four new single nucleotide polymorphisms (SNPs), one of which (-346C>T), was proved to be functional, as it decreased the promoter activity by 38p100 (-346T allele impairs DNA-binding to the YY1 transcription factor)
  • MAPPING cloned Y linked N status provisional
    Physical map
    LOC255187 5q33.1 hypothetical LOC255187 KIAA0843 FLJ36748 5q33.1 hypothetical protein FLJ36748 GRPEL2 5q33.1 GrpE-like 2, mitochondrial (E. coli) MGC3265 5q33.1 hypothetical protein MGC3265 IL17B 5q32-34 interleukin 17B CSNK1A1 13q13 casein kinase 1, alpha 1 LOC389337 5 similar to hypothetical protein 4933429F08 PERC 5q33.1 similar to hypothetical protein 4933429F08 PDE6A 5q31.3 phosphodiesterase 6A, cGMP-specific, rod, alpha SLC26A2 5q31.3 solute carrier family 26 (sulfate transporter), member 2 TIGD6 5q32 tigger transposable element derived 6 RPS20P4 5q33-qter ribosomal protein S20 pseudogene 4 CSF1R 5q31.3 colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog RPL7P 5q33.3 ribosomal protein L7 pseudogene PDGFRB 5q31.3 platelet-derived growth factor receptor, beta polypeptide CDX1 5q31.3 caudal type homeo box transcription factor 1 SLC6A7 5q31-q32 solute carrier family 6 (neurotransmitter transporter, L-proline), member 7 CAMK2A 5q33.2 calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha LOC340075 5q33.1 similar to RIKEN cDNA 9330196J05 TCOF1 5q32-q33.1 Treacher Collins-Franceschetti syndrome 1 CD74 5q31.3 CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated) RPS14 5q32 ribosomal protein S14 NDST1 5q31.3-q32 N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 SYNPO 5q33.1 synaptopodin MYOZ3 5q33.1 myozenin 3 FLJ10290 5q33.1 hypothetical protein FLJ10290 DCTN4 5q31-q32 dynactin 4 (p62) NID67 5q33.1 putative small membrane protein NID67 LRG47 5q33.1 LRG-47-like protein ZNF300 21 zinc finger protein 300 GPX3 5q23 glutathione peroxidase 3 (plasma) TNIP1 5q32-q33.1 TNFAIP3 interacting protein 1 ANXA6 5q32 annexin A6 DKFZP434C171 5q33.1 DKFZP434C171 protein GM2A 5q32 GM2 ganglioside activator protein SLC36A3 5q33.1 solute carrier family 36 (proton/amino acid symporter), member 3 SLC36A2 5q33.1 solute carrier family 36 (proton/amino acid symporter), member 2 LOC391840 5 similar to Thyroid hormone receptor-associated protein complex 240 kDa component (Trap240) (Activator-recruited cofactor 250 kDa component) (ARC250) LOC391841 5 similar to hypothetical protein DKFZp761H0421 SLC36A1 5q33.1 solute carrier family 36 (proton/amino acid symporter), member 1 FAT2 5q31-q32 FAT tumor suppressor homolog 2 (Drosophila)
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    26 - 4882 144.2 1411 - 2012 22317976
    also called VIa, variant 2/isoform b
    26 - 4885 144.3 1412 - 2012 22317976
    also called VIa or variant 6/isoform f
    18 - 3877 96.63 958 - 2012 22317976
    also called variant 3/isoform c
    27 - 5113 153 1488 - 2012 22317976
  • also called variant 4/isoform d
  • exon 6A but not 16A
  • containing basic and acidic domains similar to 10 other exons
  • a nuclear localization signal (NLS) which does not, however, alter the nucleolar localization
  • 26 - 5002 148.2 1451 - 2012 22317976
    also called XIX or variant 5/isoform e
    26 - 4999 148 1450 - 2012 22317976
    also called variant 7/isoform g
    EXPRESSION
    Type widely
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestiveintestinesmall intestine   
    Reproductivefemale systemovary   
     female systembreastmammary gland  
    Respiratorylung    
    Skin/Tegumentskin    
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Connectivebone   
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    physiological period embryo, fetal, pregnancy
    Text several tissues with a peak expression in the branchial arches, stem cells
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • a N-terminus, with a LIS1 homolog motif and repeating units of acidic and basic residues each containing a large number of putative casein kinase 2 and protein kinase C phosphorylation sites
  • 11 repetitive motifs coded by exon 6A-16 subject to phosphorylation by casein-kinase 2
  • a three-domain structure with nucleolar localization signals in the C-terminus
  • conjugated PhosphoP
    HOMOLOGY
    interspecies homolog to murine Tcof1
    intraspecies homolog to phosphonuclear protein,NOLC1
    Homologene
    FAMILY
    CATEGORY regulatory , structural protein , transport
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,cytoplasm
    intracellular,nucleus,chromatin/chromosome
    intracellular,nucleus,nucleolus
    text colocalizing with UBTF in the condensed chromosome of mitotic cells
    basic FUNCTION
  • putatively involved in early embryonic development, also in nuclear cytoplasmic shuttle
  • playing a role in craniofacial morphogenesis
  • involved in ribosomal DNA gene transcription by interacting with upstream binding factor(UBTF)and in involved in pre-rRNA methylation
  • required cell-autonomously for the formation and proliferation of neural crest cells and regulating
  • proliferation by controlling the production of mature ribosomes
  • unique spatiotemporal regulator of ribosome biogenesis
  • TCOF1 and PLK1 are critically required for proper cortical neurogenesis, which has important implications in the regulation of mammalian brain size and the pathogenesis of congenital
  • acts as a modifier of PAX3 during enteric nervous system development and in the pathogenesis of colonic aganglionosis
  • TCOF1-mediated NBN recruitment into the nucleoli regulates rRNA silencing in trans in the presence of distant chromosome breaks
  • is a DDR factor that could cooperate with ATM and NBN to suppress inappropriate rDNA transcription and maintain genomic integrity after DNA damage
  • CELLULAR PROCESS cell organization/biogenesis
    PHYSIOLOGICAL PROCESS development , cellular trafficking transport
    text nuclear-cytoplasmic transport
    PATHWAY
    metabolism
    signaling sensory transduction/vision
    a component
    INTERACTION
    DNA
    RNA
    small molecule
    protein
  • interacting with UBTF( affecting transcription of the ribosomal DNA gene)
  • TCOF1 associates with upstream binding factor (UBTF) to regulate rRNA gene (rDNA) transcription
  • TCOF1 and PLK1 are novel regulators of spindle fidelity, mitotic progression, and proliferation in the maintenance and localization of neural progenitor cells
  • interaction between the DDR factor NBN and TCOF1, a nucleolar protein that regulates ribosomal DNA (rDNA) transcription
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) TCS
    Susceptibility to isolated cleft palate with maternal transmission
    Variant & Polymorphism SNP increasing the risk of isolated cleft palate with maternal transmission
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS