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Aliases for TCOF1 Gene

Aliases for TCOF1 Gene

  • Treacle Ribosome Biogenesis Factor 1 2 3 5
  • Treacher Collins-Franceschetti Syndrome 1 2 3
  • Treacher Collins Syndrome Protein 3 4
  • Nucleolar Trafficking Phosphoprotein 3
  • Treacle Protein 3
  • Treacle 3
  • MFD1 3
  • TCS1 3
  • TCS 3

External Ids for TCOF1 Gene

Previous GeneCards Identifiers for TCOF1 Gene

  • GC05P149806
  • GC05P150198
  • GC05P149720
  • GC05P149765
  • GC05P149717
  • GC05P144885

Summaries for TCOF1 Gene

Entrez Gene Summary for TCOF1 Gene

  • This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been associated with Treacher Collins syndrome, a disorder which includes abnormal craniofacial development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

GeneCards Summary for TCOF1 Gene

TCOF1 (Treacle Ribosome Biogenesis Factor 1) is a Protein Coding gene. Diseases associated with TCOF1 include Treacher Collins Syndrome 1 and Tcof1-Related Treacher Collins Syndrome. Among its related pathways are Ribosome biogenesis in eukaryotes. GO annotations related to this gene include poly(A) RNA binding and transporter activity.

UniProtKB/Swiss-Prot for TCOF1 Gene

  • Nucleolar protein that acts as a regulator of RNA polymerase I by connecting RNA polymerase I with enzymes responsible for ribosomal processing and modification (PubMed:12777385, PubMed:26399832). Required for neural crest specification: following monoubiquitination by the BCR(KBTBD8) complex, associates with NOLC1 and acts as a platform to connect RNA polymerase I with enzymes responsible for ribosomal processing and modification, leading to remodel the translational program of differentiating cells in favor of neural crest specification (PubMed:26399832).

Gene Wiki entry for TCOF1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TCOF1 Gene

Genomics for TCOF1 Gene

Regulatory Elements for TCOF1 Gene

Enhancers for TCOF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G150404 1.7 FANTOM5 ENCODE dbSUPER 16.5 +53.1 53072 13.3 HDGF PKNOX1 MLX WRNIP1 ZFP64 SIN3A YBX1 FEZF1 YY1 ZNF207 RPS14 TCOF1 CD74 CAMK2A ZNF300P1 RBM22 SYNPO DCTN4 ZNF300 GC05M150413
GH05G150316 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11.1 -37.5 -37493 8.0 FOXA2 CREB3L1 ARNT SIN3A FEZF1 ZNF766 FOS KLF13 REST SMARCB1 PDGFRB CAMK2A TCOF1 SLC6A7 CDX1 CSF1R SYNPO ARSI
GH05G150133 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.3 -216.0 -216026 15.5 PKNOX1 FOXA2 MLX CREB3L1 ARNT ARID4B DMAP1 FEZF1 YY1 ZNF766 CDX1 SLC6A7 CSF1R TCOF1 CAMK2A PDGFRB RPS14 SYNPO
GH05G150065 1.9 FANTOM5 Ensembl ENCODE dbSUPER 9.4 -291.3 -291315 2.6 FOXA2 PKNOX1 CREB3L1 ARNT ARID4B ZNF766 FOS KLF13 SP3 SP5 HMGXB3 TIGD6 PCYOX1L CSF1R PDGFRB CDX1 PDE6A ENSG00000200334 TCOF1 CAMK2A
GH05G150496 1.7 Ensembl ENCODE dbSUPER 10.1 +150.4 150421 24.1 MLX ZFP64 DMAP1 FEZF1 YY1 ZNF143 ZNF263 SP3 MEF2D RCOR2 NDST1 ZNF300 HMGXB3 ZNF300P1 NDST1-AS1 RPL7P1 RPS14 SYNPO ENSG00000253852 TIGD6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TCOF1 on UCSC Golden Path with GeneCards custom track

Promoters for TCOF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000188961 261 1401 HDGF PKNOX1 ATF1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 YY1 ETS1

Genomic Location for TCOF1 Gene

Chromosome:
5
Start:
150,357,639 bp from pter
End:
150,400,308 bp from pter
Size:
42,670 bases
Orientation:
Plus strand

Genomic View for TCOF1 Gene

Genes around TCOF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TCOF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TCOF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TCOF1 Gene

Proteins for TCOF1 Gene

  • Protein details for TCOF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13428-TCOF_HUMAN
    Recommended name:
    Treacle protein
    Protein Accession:
    Q13428
    Secondary Accessions:
    • A0JLU0
    • B4E111
    • Q6SC72
    • Q7Z5W9
    • Q96A52
    • Q99408
    • Q99860

    Protein attributes for TCOF1 Gene

    Size:
    1488 amino acids
    Molecular mass:
    152106 Da
    Quaternary structure:
    • Heterodimer; heterodimerizes with NOLC1 following monoubiquitination (PubMed:26399832). Part of a large pre-ribosomal ribonucleoprotein (RNP) complex, that consists of at least 62 ribosomal proteins, 45 nonribosomal proteins and both pre-rRNA and mature rRNA species. Within this complex directly interacts with NOP56 in an RNA-independent manner (PubMed:12777385).
    SequenceCaution:
    • Sequence=AAH16144.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Alternative splice isoforms for TCOF1 Gene

neXtProt entry for TCOF1 Gene

Post-translational modifications for TCOF1 Gene

  • Ubiquitinated. Monoubiquitination by the BCR(KBTBD8) complex promotes the formation of a NOLC1-TCOF1 complex that acts as a platform to connect RNA polymerase I with enzymes responsible for ribosomal processing and modification, leading to remodel the translational program of differentiating cells in favor of neural crest specification (PubMed:26399832).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TCOF1 Gene

Domains & Families for TCOF1 Gene

Suggested Antigen Peptide Sequences for TCOF1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TCOF1: view

No data available for Gene Families and UniProtKB/Swiss-Prot for TCOF1 Gene

Function for TCOF1 Gene

Molecular function for TCOF1 Gene

UniProtKB/Swiss-Prot Function:
Nucleolar protein that acts as a regulator of RNA polymerase I by connecting RNA polymerase I with enzymes responsible for ribosomal processing and modification (PubMed:12777385, PubMed:26399832). Required for neural crest specification: following monoubiquitination by the BCR(KBTBD8) complex, associates with NOLC1 and acts as a platform to connect RNA polymerase I with enzymes responsible for ribosomal processing and modification, leading to remodel the translational program of differentiating cells in favor of neural crest specification (PubMed:26399832).

Gene Ontology (GO) - Molecular Function for TCOF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001042 RNA polymerase I core binding IDA 26399832
GO:0003723 RNA binding IDA 22658674
GO:0005215 transporter activity TAS 9096354
GO:0005515 protein binding IPI 17620599
GO:0046982 protein heterodimerization activity IPI 26399832
genes like me logo Genes that share ontologies with TCOF1: view
genes like me logo Genes that share phenotypes with TCOF1: view

Human Phenotype Ontology for TCOF1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TCOF1 Gene

MGI Knock Outs for TCOF1:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TCOF1 Gene

Localization for TCOF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TCOF1 Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TCOF1 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1
endosome 1

Gene Ontology (GO) - Cellular Components for TCOF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IDA --
GO:0005730 nucleolus TAS,IDA 15249688
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with TCOF1: view

Pathways & Interactions for TCOF1 Gene

genes like me logo Genes that share pathways with TCOF1: view

Pathways by source for TCOF1 Gene

1 KEGG pathway for TCOF1 Gene

Gene Ontology (GO) - Biological Process for TCOF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 9096354
GO:0006417 regulation of translation IMP 26399832
GO:0006810 transport IEA --
GO:0014029 neural crest formation IMP 26399832
GO:0014032 neural crest cell development IMP 26399832
genes like me logo Genes that share ontologies with TCOF1: view

No data available for SIGNOR curated interactions for TCOF1 Gene

Drugs & Compounds for TCOF1 Gene

(1) Drugs for TCOF1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for TCOF1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TCOF1: view

Transcripts for TCOF1 Gene

Unigene Clusters for TCOF1 Gene

Treacher Collins-Franceschetti syndrome 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for TCOF1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14a · 14b · 14c ^ 15a · 15b · 15c ^
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

ExUns: 16 ^ 17 ^ 18a · 18b ^ 19a · 19b · 19c ^ 20 ^ 21a · 21b ^ 22a · 22b · 22c ^ 23
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: -
SP11: -
SP12:
SP13:
SP14:
SP15:

Relevant External Links for TCOF1 Gene

GeneLoc Exon Structure for
TCOF1
ECgene alternative splicing isoforms for
TCOF1

Expression for TCOF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TCOF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TCOF1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (24.5), CD8 Tcells (10.8), and Lymph node (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TCOF1 Gene



Protein tissue co-expression partners for TCOF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TCOF1 Gene:

TCOF1

SOURCE GeneReport for Unigene cluster for TCOF1 Gene:

Hs.519672

Evidence on tissue expression from TISSUES for TCOF1 Gene

  • Skin(4.6)
  • Liver(4.4)
  • Eye(4.3)
  • Nervous system(4.1)
  • Lung(3.4)
  • Blood(2.6)
  • Intestine(2.5)
  • Heart(2.2)
  • Muscle(2.2)
  • Thyroid gland(2.1)
  • Lymph node(2)
  • Spleen(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TCOF1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • scalp
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with TCOF1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for TCOF1 Gene

Orthologs for TCOF1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TCOF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TCOF1 34 35
  • 97.67 (n)
cow
(Bos Taurus)
Mammalia TCOF1 34 35
  • 73.98 (n)
dog
(Canis familiaris)
Mammalia TCOF1 34 35
  • 71.95 (n)
rat
(Rattus norvegicus)
Mammalia Tcof1 34
  • 69.02 (n)
mouse
(Mus musculus)
Mammalia Tcof1 34 16 35
  • 67.85 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TCOF1 35
  • 31 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TCOF1 35
  • 27 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TCOF1 35
  • 28 (a)
OneToOne
Species where no ortholog for TCOF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for TCOF1 Gene

ENSEMBL:
Gene Tree for TCOF1 (if available)
TreeFam:
Gene Tree for TCOF1 (if available)

Paralogs for TCOF1 Gene

(1) SIMAP similar genes for TCOF1 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with TCOF1: view

No data available for Paralogs for TCOF1 Gene

Variants for TCOF1 Gene

Sequence variations from dbSNP and Humsavar for TCOF1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
VAR_005630 Treacher Collins syndrome 1 (TCS1) [MIM:154500]
VAR_035666 A colorectal cancer sample
rs1057517834 Pathogenic 150,393,525(+) AACAG(-/GCAG)CAGGC nc-transcript-variant, reference, frameshift-variant
rs119470016 Pathogenic 150,374,288(+) CCTCC(C/T)AGACC nc-transcript-variant, reference, stop-gained
rs119470017 Pathogenic 150,388,004(+) AGGCC(C/T)GAGCC nc-transcript-variant, reference, stop-gained

Structural Variations from Database of Genomic Variants (DGV) for TCOF1 Gene

Variant ID Type Subtype PubMed ID
esv1309088 CNV deletion 17803354
esv2114978 CNV deletion 18987734
esv2649922 CNV deletion 19546169
esv2672361 CNV deletion 23128226
esv2730915 CNV deletion 23290073
esv3289939 CNV deletion 24192839
esv3566810 CNV deletion 23714750
esv5186 CNV loss 18987735
esv6012 CNV loss 19470904
esv989812 CNV deletion 20482838
nsv1022057 CNV gain 25217958
nsv1074878 CNV deletion 25765185
nsv1123996 CNV deletion 24896259
nsv1150377 CNV deletion 26484159

Variation tolerance for TCOF1 Gene

Residual Variation Intolerance Score: 95.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.76; 91.61% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TCOF1 Gene

Human Gene Mutation Database (HGMD)
TCOF1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TCOF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TCOF1 Gene

Disorders for TCOF1 Gene

MalaCards: The human disease database

(27) MalaCards diseases for TCOF1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search TCOF1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TCOF_HUMAN
  • Treacher Collins syndrome 1 (TCS1) [MIM:154500]: A form of Treacher Collins syndrome, a disorder of craniofacial development. Treacher Collins syndrome is characterized by a combination of bilateral downward slanting of the palpebral fissures, colobomas of the lower eyelids with a paucity of eyelashes medial to the defect, hypoplasia of the facial bones, cleft palate, malformation of the external ears, atresia of the external auditory canals, and bilateral conductive hearing loss. {ECO:0000269 PubMed:9042910}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for TCOF1 Gene

Treacher Collins-Franceschetti syndrome,mandibulofacial dysostosis characterized by antimongoloid slant of eyes,coloboma of inferior lid,narrowing of the external ears and malformation of the middle ear ossicles which may lead to deafness,hypoplasia of the mandible (macrognathia) and cleft palate and macrostomia

Relevant External Links for TCOF1

Genetic Association Database (GAD)
TCOF1
Human Genome Epidemiology (HuGE) Navigator
TCOF1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TCOF1
genes like me logo Genes that share disorders with TCOF1: view

Publications for TCOF1 Gene

  1. Excess maternal transmission of markers in TCOF1 among cleft palate case-parent trios from three populations. (PMID: 18688869) Sull J.W. … Beaty T.H. (Am. J. Med. Genet. A 2008) 3 22 46 64
  2. Genotyping in 46 patients with tentative diagnosis of Treacher Collins syndrome revealed unexpected phenotypic variation. (PMID: 15340364) Teber O.A. … Wieczorek D. (Eur. J. Hum. Genet. 2004) 3 22 46 64
  3. Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome. (PMID: 12777385) Hayano T. … Takahashi N. (J. Biol. Chem. 2003) 3 4 22 64
  4. The mutational spectrum in Treacher Collins syndrome reveals a predominance of mutations that create a premature-termination codon. (PMID: 9042910) Edwards S.J. … Dixon M.J. (Am. J. Hum. Genet. 1997) 3 4 22 64
  5. Identification of the complete coding sequence and genomic organization of the Treacher Collins syndrome gene. (PMID: 9074926) Dixon J. … Dixon M.J. (Genome Res. 1997) 3 4 22 64

Products for TCOF1 Gene

  • Addgene plasmids for TCOF1

Sources for TCOF1 Gene

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