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Aliases for TCOF1 Gene

Aliases for TCOF1 Gene

  • Treacle Ribosome Biogenesis Factor 1 2 3
  • Treacher Collins-Franceschetti Syndrome 1 2 3 5
  • Treacher Collins Syndrome Protein 3 4
  • Nucleolar Trafficking Phosphoprotein 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 pulmonary fibrosis and/or bone marrow failure, telomere-related, 1. 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

  • May be involved in nucleolar-cytoplasmic transport. May play a fundamental role in early embryonic development, particularly in development of the craniofacial complex (By similarity). May participate in certain stages of ribosome biogenesis.

Gene Wiki entry for TCOF1 Gene

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

Genomics for TCOF1 Gene

Regulatory Elements for TCOF1 Gene

Promoters for TCOF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around TCOF1 on UCSC Golden Path with GeneCards custom track

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:
    • 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.
    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

Proteomics data for TCOF1 Gene at MOPED

Post-translational modifications for TCOF1 Gene

  • 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

Q13428

UniProtKB/Swiss-Prot:

TCOF_HUMAN :
  • Contains 1 LisH domain.
Domain:
  • Contains 1 LisH domain.
genes like me logo Genes that share domains with TCOF1: view

No data available for Gene Families for TCOF1 Gene

Function for TCOF1 Gene

Molecular function for TCOF1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in nucleolar-cytoplasmic transport. May play a fundamental role in early embryonic development, particularly in development of the craniofacial complex (By similarity). May participate in certain stages of ribosome biogenesis.

Gene Ontology (GO) - Molecular Function for TCOF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0044822 poly(A) RNA binding IDA 22658674
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:

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry 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
Jensen Localization Image for TCOF1 Gene COMPARTMENTS Subcellular localization image for TCOF1 gene
Compartment Confidence
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for TCOF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm 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

None

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 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, MOPED, and MaxQB for TCOF1 Gene



SOURCE GeneReport for Unigene cluster for TCOF1 Gene Hs.519672

genes like me logo Genes that share expression patterns with TCOF1: view

Protein tissue co-expression partners for TCOF1 Gene

- Elite partner

Primer Products

In Situ Assay 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
cow
(Bos Taurus)
Mammalia TCOF1 35
  • 73.98 (n)
  • 63.83 (a)
TCOF1 36
  • 64 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TCOF1 35
  • 71.95 (n)
  • 64.53 (a)
TCOF1 36
  • 64 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tcof1 35
  • 67.85 (n)
  • 57.65 (a)
Tcof1 16
Tcof1 36
  • 55 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia TCOF1 35
  • 97.67 (n)
  • 96.85 (a)
TCOF1 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tcof1 35
  • 69.02 (n)
  • 58.36 (a)
oppossum
(Monodelphis domestica)
Mammalia TCOF1 36
  • 27 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TCOF1 36
  • 31 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TCOF1 36
  • 28 (a)
OneToOne
Species with no ortholog for TCOF1:
  • 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)
VAR_005631 -
rs7713638 - 150,379,533(+) CCAGG(C/T)GAAGC nc-transcript-variant, reference, missense
rs15251 - 150,396,669(+) GAAAG(C/T)AAAGA reference, missense
VAR_005634 -

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

Variant ID Type Subtype PubMed ID
esv2649922 CNV Deletion 19546169
esv2114978 CNV Deletion 18987734
esv2730915 CNV Deletion 23290073
esv5186 CNV Deletion 18987735
esv2672361 CNV Deletion 23128226
esv989812 CNV Deletion 20482838
esv6012 CNV Loss 19470904
esv1309088 CNV Deletion 17803354

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

HapMap Linkage Disequilibrium report
TCOF1
Human Gene Mutation Database (HGMD)
TCOF1

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

Disorders for TCOF1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
treacher collins syndrome 1
  • treacher collins syndrome
pulmonary fibrosis and/or bone marrow failure, telomere-related, 1
  • pulmonary fibrosis, and/or bone marrow failure, telomere-related, 1
dyskeratosis congenita, autosomal dominant 2
  • dyskeratosis congenita, autosomal recessive 4
melanoma, cutaneous malignant, 9
  • cmm9
leukemia, acute myeloid
  • leukemia, acute myeloid, somatic
- 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 23 48 67
  2. Treacle recruits RNA polymerase I complex to the nucleolus that is independent of UBF. (PMID: 19527688) Lin C.I. … Yeh N.H. (Biochem. Biophys. Res. Commun. 2009) 3 23
  3. Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients. (PMID: 20003452) Masotti C. … Passos-Bueno M.R. (BMC Med. Genet. 2009) 3 23
  4. Detection of a novel silent deletion, a missense mutation and a nonsense mutation in TCOF1. (PMID: 19067896) Fujioka H. … Sakiyama Y. (Pediatr Int 2008) 3 23
  5. Mutations and new polymorphic changes in the TCOF1 gene of patients with oculo-auriculo-vertebral spectrum and Treacher-Collins syndrome. (PMID: 17786119) Su P.H. … Chen H.N. (Clin. Dysmorphol. 2007) 3 23

Products for TCOF1 Gene

Sources for TCOF1 Gene

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