Aliases for TCOF1 Gene
Aliases for TCOF1 Gene
External Ids for TCOF1 Gene
- HGNC: 11654
- Entrez Gene: 6949
- Ensembl: ENSG00000070814
- OMIM: 606847
- UniProtKB: Q13428
Previous GeneCards Identifiers for TCOF1 Gene
- GC05P149806
- GC05P150198
- GC05P149720
- GC05P149765
- GC05P149717
- GC05P144885
Summaries 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.
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
Enhancers for TCOF1 Gene
| GeneHancer Identifier | Score | Enhancer Sources | TSS distance (kb) | Number of Genes Away | Size (kb) | Transcription Factor Binding Sites within enhancer | Other Gene Targets for Enhancer |
|---|
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 |
|---|
ENSRs around TCOF1 on UCSC Golden Path with GeneCards custom track
Regulatory Element Products
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:
-
- 5q32 by Ensembl
- 5q32 by Entrez Gene
- 5q32 by HGNC
TCOF1 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
- 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};
Protein Expression for TCOF1 Gene
Post-translational modifications for TCOF1 Gene
Other Protein References for TCOF1 Gene
Antibody Products
- Novus Biologicals Antibodies for TCOF1
- Invitrogen Antibodies for TCOF1
- antibodies-online Antibodies for TCOF1: See all 37
- GeneTex TCOF1 antibody for TCOF1
-
Santa Cruz Biotechnology (SCBT) Antibodies for TCOF1
Protein Products
-
OriGene Purified Proteins for TCOF1
- Search Origene for MassSpec and Protein Over-expression Lysates for TCOF1
- Origene Custom Protein Services for TCOF1
- antibodies-online Proteins for TCOF1: See all 3
- Search antibodies-online for peptides
- Search GeneTex for Proteins for TCOF1
Assay Products
- antibodies-online Kits for TCOF1: See all 3
No data available for DME Specific Peptides for TCOF1 Gene
Domains & Families for TCOF1 Gene
Protein Domains for TCOF1 Gene
- InterPro:
- Blocks:
- ProtoNet:
Suggested Antigen Peptide Sequences for TCOF1 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
Q13428- Domain:
-
- Contains 1 LisH domain.
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.
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0044822 | poly(A) RNA binding | IDA | 22658674 |
Phenotypes for TCOF1 Gene
- MGI mutant phenotypes for TCOF1:
-
inferred from 1 alleles
- cellular phenotype
- mortality/aging
- endocrine/exocrine gland phenotype
- growth/size/body region phenotype
- digestive/alimentary phenotype
- respiratory system phenotype
- embryo phenotype
- nervous system phenotype
- vision/eye phenotype
- skeleton phenotype
- craniofacial phenotype
- hearing/vestibular/ear phenotype
- GenomeRNAi human phenotypes for TCOF1:
-
- shRNA abundance <= 50%
- Synthetic lethal with Ras
- Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection
- Increased shRNA abundance (Z-score > 2)
- Negative genetic interaction between KRASG13D/+ and KRAS+/-
- Decreased shRNA abundance (Z-score < -2)
- Synthetic lethal with MLN4924 (a NAE inhibitor)
- Decreased shRNA abundance
- Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after viral supernatant infection
- Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after direct virus infection
Animal Models for TCOF1 Gene
- MGI Knock Outs for TCOF1:
-
- Tcof1 tm1Mjd
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
- Search ViGene Biosciences for TCOF1
CRISPR Products
-
OriGene CRISPR knockouts for TCOF1
-
Santa Cruz Biotechnology (SCBT) CRISPR for TCOF1
- GenScript: Design CRISPR guide RNA sequences for TCOF1
miRNA for TCOF1 Gene
- miRTarBase miRNAs that target TCOF1
-
- hsa-mir-124-3p (MIRT022519)
- hsa-mir-34a-5p (MIRT025404)
- hsa-mir-7-5p (MIRT025762)
- hsa-let-7b-5p (MIRT032257)
- hsa-mir-744-5p (MIRT037490)
- hsa-mir-93-3p (MIRT038780)
- hsa-mir-615-3p (MIRT040239)
- hsa-mir-92b-3p (MIRT040570)
- hsa-mir-324-5p (MIRT043143)
- hsa-mir-151a-3p (MIRT043611)
- hsa-mir-222-3p (MIRT046740)
- hsa-mir-197-3p (MIRT048102)
- hsa-mir-92a-3p (MIRT049104)
- hsa-mir-218-5p (MIRT439477)
- hsa-mir-6857-5p (MIRT458568)
- hsa-mir-588 (MIRT458569)
- hsa-mir-4701-5p (MIRT458570)
- hsa-mir-7847-3p (MIRT458571)
- hsa-mir-6880-5p (MIRT458572)
- hsa-mir-6801-5p (MIRT458573)
- hsa-mir-4450 (MIRT458574)
- hsa-mir-3622b-5p (MIRT458575)
- hsa-mir-6851-5p (MIRT458576)
- hsa-mir-3689d (MIRT458577)
- hsa-mir-4252 (MIRT458578)
- hsa-mir-6786-5p (MIRT458579)
- hsa-mir-4257 (MIRT458580)
- hsa-mir-6847-5p (MIRT458581)
miRNA Products
- Search ViGene Biosciences for TCOF1
Inhibitory RNA Products
Clone Products
- OriGene clones in human for TCOF1
- OriGene ORF clones in human,mouse,rat for TCOF1
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- Addgene plasmids for TCOF1
Cell Line 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.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 3 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005737 | cytoplasm | IDA | -- |
Pathways & Interactions for TCOF1 Gene
More details on SuperPathways for TCOF1| Superpath | Contained pathways | |
|---|---|---|
| 1 | Ribosome biogenesis in eukaryotes |
Pathways by source for TCOF1 Gene
1 KEGG pathway for TCOF1 Gene
Interacting Proteins for TCOF1 Gene
Selected Interacting proteins:
ENSP00000421655
Q13428-TCOF_HUMAN
for TCOF1 Gene via
STRING
UniProtKB
I2D
No data available for SIGNOR curated interactions for TCOF1 Gene
Transcripts for TCOF1 Gene
mRNA/cDNA for TCOF1 Gene
- (16) REFSEQ mRNAs :
- (17) Additional mRNA sequences :
- (298) Selected AceView cDNA sequences:
- (15) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for TCOF1 Gene
CRISPR Products
-
OriGene CRISPR knockouts for TCOF1
-
Santa Cruz Biotechnology (SCBT) CRISPR for TCOF1
- GenScript: Design CRISPR guide RNA sequences for TCOF1
miRNA Products
- Search ViGene Biosciences for TCOF1
Inhibitory RNA Products
Clone Products
- OriGene clones in human for TCOF1
- OriGene ORF clones in human,mouse,rat for TCOF1
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat
- Addgene plasmids for TCOF1
Flow Cytometry Products
| 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 | ^ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| SP14: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| SP15: |
| ExUns: | 16 | ^ | 17 | ^ | 18a | · | 18b | ^ | 19a | · | 19b | · | 19c | ^ | 20 | ^ | 21a | · | 21b | ^ | 22a | · | 22b | · | 22c | ^ | 23 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | |||||||||||||||||||||||||||
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| SP7: | |||||||||||||||||||||||||||
| SP8: | |||||||||||||||||||||||||||
| SP9: | |||||||||||||||||||||||||||
| SP10: | - | ||||||||||||||||||||||||||
| SP11: | - | ||||||||||||||||||||||||||
| SP12: | |||||||||||||||||||||||||||
| SP13: | |||||||||||||||||||||||||||
| SP14: | |||||||||||||||||||||||||||
| SP15: |
Expression for TCOF1 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
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
- Elite partner
Primer Products
-
OriGene qPCR primer pairs for TCOF1
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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| cow (Bos Taurus) |
Mammalia | TCOF1 35 |
|
||
| TCOF1 36 |
|
OneToOne | |||
| dog (Canis familiaris) |
Mammalia | TCOF1 35 |
|
||
| TCOF1 36 |
|
OneToOne | |||
| mouse (Mus musculus) |
Mammalia | Tcof1 35 |
|
||
| Tcof1 16 |
|
||||
| Tcof1 36 |
|
OneToOne | |||
| chimpanzee (Pan troglodytes) |
Mammalia | TCOF1 35 |
|
||
| TCOF1 36 |
|
OneToOne | |||
| rat (Rattus norvegicus) |
Mammalia | Tcof1 35 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | TCOF1 36 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | TCOF1 36 |
|
OneToOne | |
| lizard (Anolis carolinensis) |
Reptilia | TCOF1 36 |
|
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)
Paralogs for TCOF1 Gene
(1) SIMAP similar genes for TCOF1 Gene using alignment to 7 proteins:
No data available for Paralogs for TCOF1 Gene
Variants 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 | - |
| 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 |
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
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TCOF1 Gene
Disorders for TCOF1 Gene
(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 |
|
|
| pulmonary fibrosis and/or bone marrow failure, telomere-related, 1 |
|
|
| dyskeratosis congenita, autosomal dominant 2 |
|
|
| melanoma, cutaneous malignant, 9 |
|
|
| leukemia, acute myeloid |
|
|
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
Publications for TCOF1 Gene
- 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
- 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
- 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
- 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
- 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
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- OriGene Purified Proteins for TCOF1
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- Novus Biologicals Antibodies for TCOF1
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- Addgene plasmids for TCOF1
- antibodies-online Antibodies for TCOF1: See all 37
- antibodies-online Kits for TCOF1: See all 3
- antibodies-online Proteins for TCOF1: See all 3
- Search antibodies-online for peptides
- GeneTex TCOF1 antibody for TCOF1
- Search GeneTex for Proteins for TCOF1
- Search ViGene Biosciences for TCOF1
- Search ViGene Biosciences for TCOF1
- Santa Cruz Biotechnology (SCBT) Antibodies for TCOF1
- Search Santa Cruz Biotechnology (SCBT) for TCOF1 siRNA/shRNA
- Santa Cruz Biotechnology (SCBT) CRISPR for TCOF1
Sources for TCOF1 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) I2D
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) UniGene
- (28) AceView
- (29) RNAdb
- (30) ASD
- (31) ECgene
- (32) GeneAnnot
- (33) SAGE
- (34) SOURCE
- (35) HomoloGene
- (36) PanEnsembl
- (37) euGenes
- (38) SGD
- (39) FlyBase
- (40) WormBase
- (41) Pseudogene
- (42) DGV
- (43) dbSNP
- (44) HapMap
- (45) GenAtlas
- (46) GeneTests
- (47) HGMD
- (48) GAD
- (49) LSDB
- (50) BGMUT
- (51) HuGE
- (52) eBioscience
- (53) Atlas
- (54) Cell Signaling Technology
- (55) GenBank
- (56) H-invDB
- (57) HORDE
- (58) HUGE
- (59) IMGT
- (60) Leiden
- (61) MILLIPORE
- (62) miRBase
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