Tbio CPSF6 Cleavage and polyadenylation specificity factor subunit 6

Protein Summary

Description

Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:9659921, PubMed:8626397, PubMed:14690600, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:9659921, PubMed:8626397, PubMed:14690600). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF6 enhances NUDT21/CPSF5 binding to 5'-UGUA-3' elements localized upstream of pA signals and promotes RNA looping, and hence activates directly the mRNA 3'-processing machinery (PubMed:15169763, PubMed:29276085, PubMed:21295486). Plays a role in mRNA export (PubMed:19864460). The protein encoded by this gene is one subunit of a cleavage factor required for 3' RNA cleavage and polyadenylation processing. The interaction of the protein with the RNA is one of the earliest steps in the assembly of the 3' end processing complex and facilitates the recruitment of other processing factors. The cleavage factor complex is composed of four polypeptides. This gene encodes the 68kD subunit. It has a domain organization reminiscent of spliceosomal proteins. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• Q16630
• A8K7K9
• Q53ES1
• Q9BSJ7
• Q9BW18

Gene Name

• CPSF6

Ensembl ID

• ENST00000266679
• ENSP00000266679
• ENSG00000111605
• ENST00000435070
• ENSP00000391774

Symbol

• CFIM68
• CFIM
• CFIM68
• CFIM72
• HPBRII-4
• HPBRII-7

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
protein complex	0.82
transcription factor perturbation	0.8
interacting protein	0.76
hub protein	0.75
transcription factor	0.67

Protein Classes

PANTHER Classes

Protein / Nucleic Acid Binding / Rna Binding Protein / Cleavage And Polyadenylation Specificity Factor Subunit 6

DTO Classes

Protein / Nucleic Acid Binding / Rna Binding Protein / Cleavage And Polyadenylation Specificity Factor Subunit 6

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: 94.75   (req: < 5)

Gene RIFs: 30   (req: <= 3)

Antibodies: 204   (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: 94.75   (req: >= 5)

Gene RIFs: 30   (req: > 3)

Antibodies: 204   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 11

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

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Expression Data (0 Tissues)

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No expression data found

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (208)

Explore Interacting Targets

1 – 10 of 208

• See Interactions on String-DB

JMJD6

Tchem

Family:  Enzyme

Novelty:  0.00305479

p_int:  0.999950415

p_ni:  0.000049585

Score:  0.357

Data Source:  BioPlex,STRINGDB

P4HA1

Tchem

Family:  Enzyme

Novelty:  0.01624726

p_int:  0.99989033

p_ni:  0.00010967

Data Source:  BioPlex

CPSF7

Tbio

Novelty:  0.13068955

p_int:  0.999429315

p_ni:  0.000570685

Score:  0.985

Data Source:  BioPlex,STRINGDB

ITCH

Tbio

Family:  Enzyme

Novelty:  0.00681861

p_int:  0.928059773

p_ni:  0.071940225

p_wrong:  3e-9

Score:  0.229

Data Source:  BioPlex,STRINGDB

WWP1

Tbio

Family:  Enzyme

Novelty:  0.01407874

p_int:  0.915371818

p_ni:  0.084628182

Score:  0.268

Data Source:  BioPlex,STRINGDB

RBBP6

Tbio

Family:  Enzyme

Novelty:  0.03147368

p_int:  0.886939934

p_ni:  0.113060066

Score:  0.313

Data Source:  BioPlex,STRINGDB

WWP2

Tbio

Family:  Enzyme

Novelty:  0.01935799

p_int:  0.839679222

p_ni:  0.160320778

Score:  0.225

Data Source:  BioPlex,STRINGDB

NUDT21

Tbio

Novelty:  0.02174736

p_int:  0.759109056

p_ni:  0.240890944

Score:  0.999

Data Source:  BioPlex,STRINGDB

CSTF2

Tbio

Novelty:  0.01389909

Score:  0.986

Data Source:  STRINGDB

CDC5L

Tbio

Family:  TF

Novelty:  0.00663599

Score:  0.983

Data Source:  STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (7)

Reactome (6)

KEGG (1)

Disease (R-HSA-1643685)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Disease	1105 targets	R-HSA-1643685
Reactome	Diseases of signal transduction	387 targets	R-HSA-5663202
Reactome	FGFR1 mutant receptor activation	32 targets	R-HSA-1839124
Reactome	Signaling by FGFR in disease	64 targets	R-HSA-1226099
Reactome	Signaling by FGFR1 in disease	39 targets	R-HSA-5655302

Name	Explore in Pharos	Explore in Source
Disease	1105 targets	R-HSA-1643685
Diseases of signal transduction	387 targets	R-HSA-5663202
FGFR1 mutant receptor activation	32 targets	R-HSA-1839124
Signaling by FGFR in disease	64 targets	R-HSA-1226099
Signaling by FGFR1 in disease	39 targets	R-HSA-5655302

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (22)

Functions (4)

Components (11)

Processes (7)

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1 – 4 of 4

GO Term	Evidence	Assigned by
exon-exon junction complex binding	Inferred from Direct Assay (IDA)	UniProtKB
mRNA binding	Inferred from Direct Assay (IDA)	UniProtKB
ribosomal large subunit binding	Inferred from Direct Assay (IDA)	UniProtKB
RNA binding	Inferred from High Throughput Direct Assay (HDA)	UniProtKB

Disease Associations ()

No disease associations found

GWAS Traits (22)

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1 – 5 of 22

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
monocyte count	EFO_0005091	2	1	2		88
monocyte percentage of leukocytes	EFO_0007989	2	1	2		87.7
Oral ulcer	HP_0000155	1	1	0	1.1	80.6
granulocyte percentage of myeloid white cells	EFO_0007997	1	1	1		80.4
leukocyte count	EFO_0004308	1	2	2		71.6

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
monocyte count	EFO_0005091	2		88
monocyte percentage of leukocytes	EFO_0007989	2		87.7
Oral ulcer	HP_0000155	0	1.1	80.6
granulocyte percentage of myeloid white cells	EFO_0007997	1		80.4
leukocyte count	EFO_0004308	2		71.6

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Alternative splicing
Complete proteome
Cytoplasm
Direct protein sequencing
Methylation
mRNA processing
Nucleus
Phosphoprotein
Reference proteome

GWAS Trait Find Similar Targets

No Header	No Header
Agents acting on the renin-angiotensin system use measurement
body mass index
C-reactive protein measurement
Calcium channel blocker use measurement
Diuretic use measurement
granulocyte count
granulocyte percentage of myeloid white cells
leukocyte count
lymphocyte percentage of leukocytes
monocyte count

IDG Resources

No IDG generated resources found

Orthologs (13)

1 – 5 of 13

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	cleavage and polyadenylation specific factor 6	VGNC:5347	452068
Macaque	cleavage and polyadenylation specific factor 6		718331
Mouse	cleavage and polyadenylation specific factor 6	MGI:1913948	432508
Rat	cleavage and polyadenylation specific factor 6	RGD:1304640	299811
Dog	cleavage and polyadenylation specific factor 6	VGNC:39577	474441

Species	Name	OMA	EggNOG	Inparanoid
Chimp	cleavage and polyadenylation specific factor 6
Macaque	cleavage and polyadenylation specific factor 6
Mouse	cleavage and polyadenylation specific factor 6
Rat	cleavage and polyadenylation specific factor 6
Dog	cleavage and polyadenylation specific factor 6

Publication Statistics

PubMed Score 94.75

PubMed score by year

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PubTator Score 36.79

PubTator score by year

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Related Publications

Text Mined References (47)

GeneRif Annotations (30)

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PMID	Year	Title