ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for TFRC

Gene summary

Gene information	Gene symbol	TFRC
	Gene ID	7037
	Gene name	transferrin receptor
	Synonyms	CD71\|IMD46\|T9\|TFR\|TFR1\|TR\|TRFR\|p90
	Cytomap	3q29
	Type of gene	protein-coding
	Description	transferrin receptor protein 1
	Modification date	20200313
	UniProtAcc	F8WBE5, G3V0E5, H7C3V5, P02786,
	Context

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

Gene	GO ID	GO term	PubMed ID
TFRC	GO:0006826	iron ion transport	7556058
TFRC	GO:0030890	positive regulation of B cell proliferation	26642240
TFRC	GO:0031623	receptor internalization	26642240
TFRC	GO:0033572	transferrin transport	26642240
TFRC	GO:0035690	cellular response to drug	16254249
TFRC	GO:0042102	positive regulation of T cell proliferation	26642240
TFRC	GO:0045830	positive regulation of isotype switching	26642240

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Gene structures and expression levels for TFRC

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.

ENSG00000072274

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
PCC	UP	ENST00000420415.5	TFRC-203:protein_coding:TFRC	9.810638e+01	1.614514e+00	1.896462e-07	7.914883e-05
CB	DOWN	ENST00000420415.5	TFRC-203:protein_coding:TFRC	5.973784e+02	-8.513764e-01	1.348467e-03	6.639909e-03
TC	DOWN	ENST00000420415.5	TFRC-203:protein_coding:TFRC	3.954914e+02	-1.423037e+00	7.040649e-05	1.223451e-03

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

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

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_108382	chr3	196053509:196053558:196055080:196055301:196058284:196058365	196055080:196055301
exon_skip_114321	chr3	196072003:196072152:196073930:196074125:196077064:196077122	196073930:196074125
exon_skip_170554	chr3	196074083:196074125:196075159:196075360:196077064:196077122	196075159:196075360
exon_skip_247886	chr3	196073930:196074125:196075159:196075360:196077064:196077105	196075159:196075360
exon_skip_26011	chr3	196069455:196069568:196071396:196071498:196072003:196072152	196071396:196071498
exon_skip_288822	chr3	196075159:196075360:196077064:196077122:196082043:196082090	196077064:196077122
exon_skip_293828	chr3	196072003:196072152:196073930:196074125:196077064:196077105	196073930:196074125
exon_skip_55501	chr3	196073930:196074125:196075159:196075360:196077064:196077122	196075159:196075360

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

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

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
ENST00000360110	196077064	196077122	3UTR-3CDS
ENST00000360110	196071396	196071498	Frame-shift
ENST00000392396	196071396	196071498	Frame-shift
ENST00000360110	196075159	196075360	Frame-shift
ENST00000392396	196075159	196075360	Frame-shift
ENST00000360110	196055080	196055301	In-frame
ENST00000392396	196055080	196055301	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
ENST00000360110	196071396	196071498	Frame-shift
ENST00000392396	196071396	196071498	Frame-shift
ENST00000360110	196075159	196075360	Frame-shift
ENST00000392396	196075159	196075360	Frame-shift
ENST00000360110	196055080	196055301	In-frame
ENST00000392396	196055080	196055301	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
ENST00000360110	196071396	196071498	Frame-shift
ENST00000392396	196071396	196071498	Frame-shift
ENST00000360110	196075159	196075360	Frame-shift
ENST00000392396	196075159	196075360	Frame-shift
ENST00000360110	196055080	196055301	In-frame
ENST00000392396	196055080	196055301	In-frame

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

p-ENSG00000072274_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
ENST00000360110	5128	760	196055080	196055301	1848	2068	559	632
ENST00000392396	5049	760	196055080	196055301	1961	2181	559	632

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
ENST00000360110	5128	760	196055080	196055301	1848	2068	559	632
ENST00000392396	5049	760	196055080	196055301	1961	2181	559	632

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
ENST00000360110	5128	760	196055080	196055301	1848	2068	559	632
ENST00000392396	5049	760	196055080	196055301	1961	2181	559	632

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
P02786	559	632	604	606	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	604	606	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	1	760	Chain	ID=PRO_0000174132;Note=Transferrin receptor protein 1
P02786	559	632	1	760	Chain	ID=PRO_0000174132;Note=Transferrin receptor protein 1
P02786	559	632	101	760	Chain	ID=PRO_0000292265;Note=Transferrin receptor protein 1%2C serum form
P02786	559	632	101	760	Chain	ID=PRO_0000292265;Note=Transferrin receptor protein 1%2C serum form
P02786	559	632	573	579	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	573	579	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	583	603	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	583	603	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	613	625	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	613	625	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	626	628	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	626	628	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	619	619	Mutagenesis	Note=20-fold reduced affinity for transferrin receptor. No binding to HFE. L->A
P02786	559	632	619	619	Mutagenesis	Note=20-fold reduced affinity for transferrin receptor. No binding to HFE. L->A
P02786	559	632	622	622	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. V->A
P02786	559	632	622	622	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. V->A
P02786	559	632	623	623	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. R->A
P02786	559	632	623	623	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. R->A
P02786	559	632	629	629	Mutagenesis	Note=>5-fold reduced affinity for transferrin. >10-fold reduced affinity for HFE. R->A
P02786	559	632	629	629	Mutagenesis	Note=>5-fold reduced affinity for transferrin. >10-fold reduced affinity for HFE. R->A
P02786	559	632	569	760	Region	Note=Ligand-binding
P02786	559	632	569	760	Region	Note=Ligand-binding
P02786	559	632	89	760	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P02786	559	632	89	760	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P02786	559	632	564	567	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	564	567	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	629	636	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	629	636	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS

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
P02786	559	632	604	606	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	604	606	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	1	760	Chain	ID=PRO_0000174132;Note=Transferrin receptor protein 1
P02786	559	632	1	760	Chain	ID=PRO_0000174132;Note=Transferrin receptor protein 1
P02786	559	632	101	760	Chain	ID=PRO_0000292265;Note=Transferrin receptor protein 1%2C serum form
P02786	559	632	101	760	Chain	ID=PRO_0000292265;Note=Transferrin receptor protein 1%2C serum form
P02786	559	632	573	579	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	573	579	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	583	603	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	583	603	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	613	625	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	613	625	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	626	628	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	626	628	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	619	619	Mutagenesis	Note=20-fold reduced affinity for transferrin receptor. No binding to HFE. L->A
P02786	559	632	619	619	Mutagenesis	Note=20-fold reduced affinity for transferrin receptor. No binding to HFE. L->A
P02786	559	632	622	622	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. V->A
P02786	559	632	622	622	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. V->A
P02786	559	632	623	623	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. R->A
P02786	559	632	623	623	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. R->A
P02786	559	632	629	629	Mutagenesis	Note=>5-fold reduced affinity for transferrin. >10-fold reduced affinity for HFE. R->A
P02786	559	632	629	629	Mutagenesis	Note=>5-fold reduced affinity for transferrin. >10-fold reduced affinity for HFE. R->A
P02786	559	632	569	760	Region	Note=Ligand-binding
P02786	559	632	569	760	Region	Note=Ligand-binding
P02786	559	632	89	760	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P02786	559	632	89	760	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P02786	559	632	564	567	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	564	567	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	629	636	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	629	636	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS

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
P02786	559	632	604	606	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	604	606	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	1	760	Chain	ID=PRO_0000174132;Note=Transferrin receptor protein 1
P02786	559	632	1	760	Chain	ID=PRO_0000174132;Note=Transferrin receptor protein 1
P02786	559	632	101	760	Chain	ID=PRO_0000292265;Note=Transferrin receptor protein 1%2C serum form
P02786	559	632	101	760	Chain	ID=PRO_0000292265;Note=Transferrin receptor protein 1%2C serum form
P02786	559	632	573	579	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	573	579	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	583	603	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	583	603	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	613	625	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	613	625	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	626	628	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	626	628	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	619	619	Mutagenesis	Note=20-fold reduced affinity for transferrin receptor. No binding to HFE. L->A
P02786	559	632	619	619	Mutagenesis	Note=20-fold reduced affinity for transferrin receptor. No binding to HFE. L->A
P02786	559	632	622	622	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. V->A
P02786	559	632	622	622	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. V->A
P02786	559	632	623	623	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. R->A
P02786	559	632	623	623	Mutagenesis	Note=No significant effect on binding to transferrin nor HFE. R->A
P02786	559	632	629	629	Mutagenesis	Note=>5-fold reduced affinity for transferrin. >10-fold reduced affinity for HFE. R->A
P02786	559	632	629	629	Mutagenesis	Note=>5-fold reduced affinity for transferrin. >10-fold reduced affinity for HFE. R->A
P02786	559	632	569	760	Region	Note=Ligand-binding
P02786	559	632	569	760	Region	Note=Ligand-binding
P02786	559	632	89	760	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P02786	559	632	89	760	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P02786	559	632	564	567	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	564	567	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	629	636	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS
P02786	559	632	629	636	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KAS

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

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

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SNVs in the skipped exons for TFRC

- 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

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AD stage-associated exon skippint events for TFRC

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

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

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for TFRC

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for TFRC

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P02786	approved	DB01592	Iron	small molecule	P02786
P02786	approved	DB14488	Ferrous gluconate	small molecule	P02786
P02786	approved	DB14489	Ferrous succinate	small molecule	P02786
P02786	approved	DB14490	Ferrous ascorbate	small molecule	P02786
P02786	approved	DB14491	Ferrous fumarate	small molecule	P02786
P02786	approved	DB14501	Ferrous glycine sulfate	small molecule	P02786
P02786	approved	DB14520	Tetraferric tricitrate decahydrate	small molecule	P02786

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RelatedDiseases for TFRC

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

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Gene summary for TFRC

Gene structures and expression levels for TFRC

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

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

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

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

SNVs in the skipped exons for TFRC

AD stage-associated exon skippint events for TFRC

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

Correlation with RNA binding proteins (RBPs) for TFRC

RelatedDrugs for TFRC

RelatedDiseases for TFRC