ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PFKFB3

Gene summary

Gene information	Gene symbol	PFKFB3
	Gene ID	5209
	Gene name	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
	Synonyms	IPFK2\|PFK2\|iPFK-2
	Cytomap	10p15.1
	Type of gene	protein-coding
	Description	6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 36-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase6PF-2-K/Fru-2,6-P2ase 36PF-2-K/Fru-2,6-P2ase brain/placenta-type isozymePFK/FBPase 3fructose-6-phosphate,2-kinase/fructose-2, 6-bisphosphatase
	Modification date	20200329
	UniProtAcc	A0A1W2PNV9, A0A1W2PR17, F2Z2I2, H0Y483, H0YDV0, Q16875, Q5VX20, Q5W015, Q9BQU1, Q9BQU2, Q9BQU3, Q9H178,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene

GO ID

GO term

PubMed ID

Top

Gene structures and expression levels for PFKFB3

Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

ENSG00000170525

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
STG	UP	ENST00000536985.6	PFKFB3-215:protein_coding:PFKFB3	6.783110e+00	1.690626e+00	1.399534e-03	4.592120e-02
TC	UP	ENST00000379775.9	PFKFB3-203:protein_coding:PFKFB3	2.150601e+03	9.206506e-01	1.906356e-03	1.618808e-02

Landscape of isoform expressions across multiple brain tissues between AD and control.

Top

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PFKFB3

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_139866	chr10	6224166:6224213:6224506:6224623:6226192:6226365	6224506:6224623
exon_skip_141889	chr10	6223958:6224020:6224149:6224213:6226192:6226365	6224149:6224213
exon_skip_164973	chr10	6224166:6224213:6226192:6226365:6232895:6232952	6226192:6226365
exon_skip_177944	chr10	6221404:6221527:6221641:6221745:6222855:6222984	6221641:6221745
exon_skip_182449	chr10	6216706:6216780:6217135:6217191:6219569:6219693	6217135:6217191
exon_skip_182958	chr10	6221463:6221527:6221641:6221745:6222855:6222984	6221641:6221745
exon_skip_188952	chr10	6228196:6228218:6231263:6231314:6232895:6232952	6231263:6231314
exon_skip_211520	chr10	6216125:6216191:6216706:6216780:6217135:6217177	6216706:6216780
exon_skip_242564	chr10	6226192:6226365:6228196:6228218:6232895:6232952	6228196:6228218
exon_skip_243977	chr10	6221507:6221527:6221641:6221745:6222855:6222984	6221641:6221745
exon_skip_51027	chr10	6226201:6226365:6228196:6228218:6232895:6232952	6228196:6228218
exon_skip_54844	chr10	6226192:6226365:6228196:6228218:6231263:6231305	6228196:6228218
exon_skip_58508	chr10	6224149:6224213:6225161:6225248:6226192:6226365	6225161:6225248

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information	Tissue type	Avg(PSIs) in AD	Avg(PSIs) in control	Difference (PSI)	Adj. p-value
exon_skip_188952	Mayo_TC	5.227397e-01	6.598214e-01	-1.370817e-01	3.227028e-06

Top

Open reading frame (ORF) annotation in the exon skipping event for PFKFB3

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000379775	6224149	6224213	Frame-shift
ENST00000379775	6217135	6217191	In-frame
ENST00000379775	6221641	6221745	In-frame
ENST00000379775	6226192	6226365	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000379775	6221641	6221745	In-frame
ENST00000379775	6226192	6226365	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000379775	6224149	6224213	Frame-shift
ENST00000379775	6216706	6216780	In-frame
ENST00000379775	6217135	6217191	In-frame
ENST00000379775	6221641	6221745	In-frame
ENST00000379775	6226192	6226365	In-frame

Top

Infer the effects of exon skipping event on protein functional features for PFKFB3

p-ENSG00000170525_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000379775	4500	520	6217135	6217191	773	828	147	166
ENST00000379775	4500	520	6221641	6221745	1310	1413	326	361
ENST00000379775	4500	520	6226192	6226365	1673	1845	447	505

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000379775	4500	520	6221641	6221745	1310	1413	326	361
ENST00000379775	4500	520	6226192	6226365	1673	1845	447	505

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000379775	4500	520	6216706	6216780	698	771	122	147
ENST00000379775	4500	520	6217135	6217191	773	828	147	166
ENST00000379775	4500	520	6221641	6221745	1310	1413	326	361
ENST00000379775	4500	520	6226192	6226365	1673	1845	447	505

Lost protein functional features of individual exon skipping events in ROSMAP.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q16875	147	166	155	155	Active site	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16875	147	166	147	154	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	147	166	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	147	166	157	163	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	147	166	165	169	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	147	166	164	169	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16316985,ECO:0000269\|PubMed:17499765,ECO:0000269\|PubMed:22275052;Dbxref=PMID:16316985,PMID:17499765,PMID:22275052
Q16875	147	166	1	245	Region	Note=6-phosphofructo-2-kinase
Q16875	326	361	334	334	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	348	348	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	352	352	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	326	361	327	329	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	334	340	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	342	350	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	345	348	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P07953
Q16875	326	361	246	520	Region	Note=Fructose-2%2C6-bisphosphatase
Q16875	326	361	352	354	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	447	505	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	447	505	455	457	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2AXN
Q16875	447	505	461	461	Modified residue	Note=Phosphoserine%3B by AMPK;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:23186163,ECO:0000269\|PubMed:12065600;Db
Q16875	447	505	463	463	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q16875	447	505	467	467	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231;Dbxref=PMID:18669648,PMID:19690332,PMID:20068231
Q16875	447	505	471	471	Modified residue	Note=Phosphothreonine%3B by PKC;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16875	447	505	246	520	Region	Note=Fructose-2%2C6-bisphosphatase

Lost protein functional features of individual exon skipping events in MSBB.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q16875	326	361	334	334	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	348	348	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	352	352	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	326	361	327	329	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	334	340	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	342	350	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	345	348	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P07953
Q16875	326	361	246	520	Region	Note=Fructose-2%2C6-bisphosphatase
Q16875	326	361	352	354	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	447	505	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	447	505	455	457	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2AXN
Q16875	447	505	461	461	Modified residue	Note=Phosphoserine%3B by AMPK;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:23186163,ECO:0000269\|PubMed:12065600;Db
Q16875	447	505	463	463	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q16875	447	505	467	467	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231;Dbxref=PMID:18669648,PMID:19690332,PMID:20068231
Q16875	447	505	471	471	Modified residue	Note=Phosphothreonine%3B by PKC;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16875	447	505	246	520	Region	Note=Fructose-2%2C6-bisphosphatase

Lost protein functional features of individual exon skipping events in Mayo.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q16875	122	147	125	125	Active site	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16875	122	147	120	126	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	122	147	147	154	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	122	147	127	127	Binding site	Note=Fructose 6-phosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16316985;Dbxref=PMID:16316985
Q16875	122	147	133	133	Binding site	Note=Fructose 6-phosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16316985;Dbxref=PMID:16316985
Q16875	122	147	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	122	147	131	144	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	122	147	1	245	Region	Note=6-phosphofructo-2-kinase
Q16875	122	147	136	136	Sequence conflict	Note=M->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q16875	122	147	141	141	Sequence conflict	Note=A->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q16875	147	166	155	155	Active site	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q16875	147	166	147	154	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	147	166	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	147	166	157	163	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	147	166	165	169	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	147	166	164	169	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16316985,ECO:0000269\|PubMed:17499765,ECO:0000269\|PubMed:22275052;Dbxref=PMID:16316985,PMID:17499765,PMID:22275052
Q16875	147	166	1	245	Region	Note=6-phosphofructo-2-kinase
Q16875	326	361	334	334	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	348	348	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	352	352	Binding site	Note=Fructose 2%2C6-bisphosphate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25849762;Dbxref=PMID:25849762
Q16875	326	361	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	326	361	327	329	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	334	340	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	342	350	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	326	361	345	348	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P07953
Q16875	326	361	246	520	Region	Note=Fructose-2%2C6-bisphosphatase
Q16875	326	361	352	354	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5AK0
Q16875	447	505	1	520	Chain	ID=PRO_0000179968;Note=6-phosphofructo-2-kinase/fructose-2%2C6-bisphosphatase 3
Q16875	447	505	455	457	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2AXN
Q16875	447	505	461	461	Modified residue	Note=Phosphoserine%3B by AMPK;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:23186163,ECO:0000269\|PubMed:12065600;Db
Q16875	447	505	463	463	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q16875	447	505	467	467	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231;Dbxref=PMID:18669648,PMID:19690332,PMID:20068231
Q16875	447	505	471	471	Modified residue	Note=Phosphothreonine%3B by PKC;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q16875	447	505	246	520	Region	Note=Fructose-2%2C6-bisphosphatase

Top

3'-UTR located exon skipping events that lost miRNA binding sites in PFKFB3

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

Top

SNVs in the skipped exons for PFKFB3

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

Top

AD stage-associated exon skippint events for PFKFB3

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PFKFB3

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
TC	exon_skip_242564	rs12571538	chr10:6136998	4.498294e-06	1.275431e-03

Top

Correlation with RNA binding proteins (RBPs) for PFKFB3

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
IFG	PABPN1L	exon_skip_164973	4.222890e-01	2.821718e-02
TC	CELF1	exon_skip_242564	4.762130e-01	1.955722e-10

Top

RelatedDrugs for PFKFB3

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

Top

RelatedDiseases for PFKFB3

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

Home

Download

Statistics

Landscape

Help

Contact