Tbio TCOF1 Treacle protein

Protein Summary

Description

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). 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]

Uniprot Accession IDs

• Q13428
• A0JLU0
• B4E111
• Q6SC72
• Q7Z5W9
• Q96A52
• Q99408
• Q99860

Gene Name

• TCOF1

Ensembl ID

• ENST00000323668
• ENSP00000325223
• ENSG00000070814
• ENST00000377797
• ENSP00000367028
• ENST00000394269
• ENSP00000377811
• ENST00000427724
• ENSP00000390717
• ENST00000439160
• ENSP00000406888
• ENST00000445265
• ENSP00000409944
• ENST00000504761
• ENSP00000421655
• ENST00000642994
• ENSP00000494375
• ENST00000643257
• ENSP00000493815

Symbol

• TCS
• MFD1
• TCS1
• treacle

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
drug perturbation	1
disease perturbation	0.96
interacting protein	0.95
co-expressed gene	0.93
transcription factor perturbation	0.91

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Target Illumination GWAS Analytics (TIGA)

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

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IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 149.8   (req: < 5)

Gene RIFs: 31   (req: <= 3)

Antibodies: 177   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 149.8   (req: >= 5)

Gene RIFs: 31   (req: > 3)

Antibodies: 177   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 9

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

GWAS Traits (2)

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GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
neutrophil count	EFO_0004833	1	1	1		33.1
gut microbiome measurement	EFO_0007874	1	1	0	3.3	21.5

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
neutrophil count	EFO_0004833	1		33.1
gut microbiome measurement	EFO_0007874	0	3.3	21.5

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Orthologs (9)

1 – 5 of 9

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	treacle ribosome biogenesis factor 1	VGNC:13606	471696
Macaque	treacle ribosome biogenesis factor 1		664735
Mouse	treacle ribosome biogenesis factor 1	MGI:892003	21453
Rat	treacle ribosome biogenesis factor 1	RGD:1309850	291571
Dog	treacle ribosome biogenesis factor 1	VGNC:47206	403592

Species	Name	OMA	EggNOG	Inparanoid
Chimp	treacle ribosome biogenesis factor 1
Macaque	treacle ribosome biogenesis factor 1
Mouse	treacle ribosome biogenesis factor 1
Rat	treacle ribosome biogenesis factor 1
Dog	treacle ribosome biogenesis factor 1

Protein Structure (0 Structures, 1 AlphaFold Model)

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Representation

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Color Scheme

  target   atomindex   bfactor   chainname   electrostatic   element   hydrophobicity   resname   sstruc

AF-Q13428-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

Pathways (1)

KEGG (1)

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Data Source	Name	Explore in Pharos	Explore in Source
KEGG	Ribosome biogenesis in eukaryotes	77 targets	path:hsa03008

Name	Explore in Pharos	Explore in Source
Ribosome biogenesis in eukaryotes	77 targets	path:hsa03008

Gene Ontology Terms (13)

Functions (5)

Components (4)

Processes (4)

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10

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GO Term	Evidence	Assigned by
RNA polymerase I core binding	Inferred from Direct Assay (IDA)	UniProtKB
protein heterodimerization activity	Inferred from Physical Interaction (IPI)	UniProtKB
scaffold protein binding	Inferred from Physical Interaction (IPI)	CAFA
RNA binding	Inferred from High Throughput Direct Assay (HDA)	UniProtKB
transporter activity	Traceable Author Statement (TAS)	ProtInc

Protein-Protein Interactions (92)

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1 – 10 of 92

• See Interactions on String-DB

CAMKV

Tbio

Family:  Kinase

Novelty:  0.17794181

p_int:  0.982570814

p_ni:  0.017429186

Data Source:  BioPlex

PIP4K2A

Tbio

Family:  Kinase

Novelty:  0.01130885

p_int:  0.970451891

p_ni:  0.029548109

Data Source:  BioPlex

DENND2D

Tbio

Novelty:  0.16496649

p_int:  0.967086142

p_ni:  0.032913858

Score:  0.201

Data Source:  BioPlex,STRINGDB

FGF12

Tbio

Novelty:  0.02094849

p_int:  0.932725229

p_ni:  0.067274771

p_wrong:  1e-9

Data Source:  BioPlex

PLCD4

Tbio

Family:  Enzyme

Novelty:  0.07014141

p_int:  0.91340282

p_ni:  0.086597181

Data Source:  BioPlex

ARRB1

Tbio

Novelty:  0.00262758

p_int:  0.778818439

p_ni:  0.221181561

Score:  0.28

Data Source:  BioPlex,STRINGDB

TARBP2

Tbio

Novelty:  0.01485994

Score:  0.802

Data Source:  STRINGDB

POLR1D

Tbio

Family:  Enzyme

Novelty:  0.01598347

Score:  0.753

Data Source:  STRINGDB

POLR1D

Tbio

Novelty:  0.01598347

Score:  0.753

Data Source:  STRINGDB

PRKRA

Tbio

Family:  Kinase

Novelty:  0.02115618

Score:  0.744

Data Source:  STRINGDB

Publication Statistics

PubMed Score  149.80

PubMed score by year

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PubTator Score  171.84

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

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UniProt Keyword Find Similar Targets

No Header	No Header
Acetylation
Alternative splicing
Complete proteome
Direct protein sequencing
Disease mutation
Isopeptide bond
Nucleus
Phosphoprotein
Polymorphism
Reference proteome

GWAS Trait Find Similar Targets

No Header	No Header
gut microbiome measurement
neutrophil count

MGI Phenotype Find Similar Targets

No Header	No Header
behavior/neurological phenotype
cellular phenotype
craniofacial phenotype
digestive/alimentary phenotype
embryo phenotype
endocrine/exocrine gland phenotype
growth/size/body region phenotype
hearing/vestibular/ear phenotype
limbs/digits/tail phenotype
mortality/aging