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Editing gene: USP19 (CAeditome ID:10869)

Gene summary for USP19

Gene summary

Gene information	Gene symbol	USP19
	Gene ID	10869
	Gene name	ubiquitin specific peptidase 19
	Synonyms	ZMYND9
	Cytomap	3p21.31
	Type of gene	protein-coding
	Description	ubiquitin carboxyl-terminal hydrolase 19deubiquitinating enzyme 19ubiquitin specific protease 19ubiquitin thioesterase 19ubiquitin thiolesterase 19ubiquitin-specific-processing protease 19zinc finger MYND domain-containing protein 9
	Modification date	20210529
	UniProtAcc	O94966
	Context

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

Gene	GO ID	GO term	PubMed ID
USP19	GO:0004843	Ubiquitin carboxyl-terminal hydrolase 19	19465887
USP19	GO:0051879	Ubiquitin carboxyl-terminal hydrolase 19	24356957
USP19	GO:0030433	Ubiquitin carboxyl-terminal hydrolase 19	19465887
USP19	GO:0005789	Ubiquitin carboxyl-terminal hydrolase 19	19465887
USP19	GO:0005829	Ubiquitin carboxyl-terminal hydrolase 19	24356957

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RNA A-to-I events for USP19

RNA A-to-I editing events across TCGA 33 cancers data sets based on Ensembl gene isoform structure.

RNA editing frequencies across 33 cancers of gene: ENSG00000172046.17

RNA A-to-I editing events in Cancer.

CAediting_278213(49118013, -), CAediting_278214(49118120, -),

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RNA editing positional annotations for USP19 using Annovar

Protein coding RNA editing(s).

CAeditome ID	Position	Variant type	ENST	NTchange	AAchange	SIFT_score	Polyphen2_HVAR_score	PROVEAN_pred
CAediting_278213	chr3_49118013_-	nonsynonymous SNV	ENST00000306026.5	c.A232G	p.T78A	D	B	N
CAediting_278213	chr3_49118013_-	nonsynonymous SNV	ENST00000398888.5	c.A232G	p.T78A	D	B	N
CAediting_278213	chr3_49118013_-	nonsynonymous SNV	ENST00000417901.4	c.A232G	p.T78A	D	B	N
CAediting_278213	chr3_49118013_-	nonsynonymous SNV	ENST00000434032.5	c.A232G	p.T78A	D	B	N
CAediting_278213	chr3_49118013_-	nonsynonymous SNV	ENST00000453664.4	c.A232G	p.T78A	D	B	N
CAediting_278214	chr3_49118120_-	nonsynonymous SNV	ENST00000306026.5	c.A125G	p.E42G	D	B	N
CAediting_278214	chr3_49118120_-	nonsynonymous SNV	ENST00000398888.5	c.A125G	p.E42G	D	B	N
CAediting_278214	chr3_49118120_-	nonsynonymous SNV	ENST00000417901.4	c.A125G	p.E42G	D	B	N
CAediting_278214	chr3_49118120_-	nonsynonymous SNV	ENST00000434032.5	c.A125G	p.E42G	D	B	N
CAediting_278214	chr3_49118120_-	nonsynonymous SNV	ENST00000453664.4	c.A125G	p.E42G	D	B	N

Gene structure information of RNA editing(s).

CAeditome ID	Position	Variant type
CAediting_278213	chr3_49118013_-	exonic
CAediting_278214	chr3_49118120_-	exonic

Repat-regional RNA editing(s).

CAeditome ID	Position	Repeat family	Repeat sub family	Repeat name
CAediting_278213	chr3_49118013_-	SINE	Alu	AluJr
CAediting_278214	chr3_49118120_-	SINE	Alu	AluJr

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RNA A-to-I editing events in the alternative splicing sites for USP19

RNA A-to-I editing(s) in the alternative splicing sites.

AStype	CAeditomID	Editing position	AS position	AS direction	Exonic location	Wildtype sequence	Wildtype splicing strength	RNA edited sequence	RNA edited splicing strength
ES	CAediting_278214	chr3_49118120_-	49118112:49118134	3SS	0+6i	TATTTTTTTTTTAGAGACAGGGT	-3.91	TATTTTTTTTTTAGGGACAGGGT	0.01
ES	CAediting_278214	chr3_49118120_-	49118116:49118138	3SS	0+2i	TTCTTATTTTTTTTTTAGAGACA	-0.59	TTCTTATTTTTTTTTTAGGGACA	-8.54
ES	CAediting_278214	chr3_49118120_-	49118118:49118140	3SS	1+0i	TTTTCTTATTTTTTTTTTAGAGA	10.16	TTTTCTTATTTTTTTTTTAGGGA	11.76

Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000172046.17.USP19.

Correlation between RNA A-to-I editing and PSI for ENSG00000172046.17.USP19.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for USP19

Differential gene expressions between RNA A-to-I edited and non-edited tumor samples.
* The grey color means N/A.

Correlation between RNA A-to-I editing and gene expression.

- Differentially expressed gene between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.

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Protein coding region RNA A-to-I editings for USP19

- Lollipop plot for RNA A-to-I editings across protein structure.
* Click on the image to enlarge it in a new window.

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The effects of the RNA editing to the miRNA binding sites for USP19

**If you are searching a miRNA gene with RNA editing events in its seed regions, please see the search pages of miRNA targets to discover the effects of this RNA editing event to miRNA regulations. For more information, please check the files in the Download page.

RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in lncRNA gained miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in lncRNA lost miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs gained binding to lncRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs lost binding to lncRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.

CAeditom_ID	Position	ENSG	ENST	miRNA	Targetscan start	Targetscan end	Targetscan score	Miranda start	Miranda end	Miranda score	Miranda energy
CAediting_1368054	chr19_46709310_-	ENSG00000172046.17	ENST00000398896	hsa-miR-320e	49108354	49108360	7mer-m8	49108353	49108370	140	-15.02
CAediting_604450	chr7_133034877_-	ENSG00000172046.17	ENST00000398896	hsa-miR-3654	49108211	49108216	6mer	49108210	49108228	141	-24.88
CAediting_1368054	chr19_46709310_-	ENSG00000172046.17	ENST00000417901	hsa-miR-320e	49108354	49108360	7mer-m8	49108353	49108370	140	-15.02
CAediting_604450	chr7_133034877_-	ENSG00000172046.17	ENST00000417901	hsa-miR-3654	49108211	49108216	6mer	49108210	49108228	141	-24.88
CAediting_1368054	chr19_46709310_-	ENSG00000172046.17	ENST00000453664	hsa-miR-320e	49108354	49108360	7mer-m8	49108353	49108370	140	-15.02
CAediting_604450	chr7_133034877_-	ENSG00000172046.17	ENST00000453664	hsa-miR-3654	49108211	49108216	6mer	49108210	49108228	141	-24.88
CAediting_524911	chr7_5495852_-	ENSG00000172046.17	ENST00000398888	hsa-miR-589-3p	49108753	49108760	8mer-1a	49108753	49108773	142	-15.73
CAediting_524911	chr7_5495852_-	ENSG00000172046.17	ENST00000434032	hsa-miR-589-3p	49108753	49108760	8mer-1a	49108753	49108773	142	-15.73

RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for USP19

- RNA A-to-I editing in mRNA.
* Click on the image to enlarge it in a new window.

ENST	ENST type	RNA structure without RNA A-to-I editing.	RNA structure with RNA A-to-I editing.
ENST00000306026.5	protein_coding
ENST00000398888.5	protein_coding
ENST00000417901.4	protein_coding
ENST00000434032.5	protein_coding
ENST00000453664.4	protein_coding
ENST00000465902.1	processed_transcript
ENST00000488993.4	processed_transcript
ENST00000491859.4	processed_transcript

RNA A-to-I editing in RNA structures for Minimum free energy (MFE).

CAeditom_ID	ENST	Editing_Position	MFE_withoneAI	MFE_withoutAI	MFE_withmultipleAI
CAediting_278213	ENST00000306026.5	chr3_49118013_-	-836.90	-835.00	-836.90
CAediting_278214	ENST00000306026.5	chr3_49118120_-	-835.00	-835.00	-836.90
CAediting_278213	ENST00000398888.5	chr3_49118013_-	-1908.40	-1906.50	-1908.40
CAediting_278214	ENST00000398888.5	chr3_49118120_-	-1906.50	-1906.50	-1908.40
CAediting_278213	ENST00000417901.4	chr3_49118013_-	-1964.90	-1963.00	-1964.90
CAediting_278214	ENST00000417901.4	chr3_49118120_-	-1963.00	-1963.00	-1964.90
CAediting_278213	ENST00000434032.5	chr3_49118013_-	-2014.10	-2012.20	-2014.10
CAediting_278214	ENST00000434032.5	chr3_49118120_-	-2012.20	-2012.20	-2014.10
CAediting_278213	ENST00000453664.4	chr3_49118013_-	-1991.60	-1989.70	-1991.60
CAediting_278214	ENST00000453664.4	chr3_49118120_-	-1989.70	-1989.70	-1991.60
CAediting_278213	ENST00000465902.1	chr3_49118013_-	-264.70	-262.80	-264.70
CAediting_278214	ENST00000465902.1	chr3_49118120_-	-262.80	-262.80	-264.70
CAediting_278213	ENST00000488993.4	chr3_49118013_-	-520.20	-520.00	-520.20
CAediting_278214	ENST00000488993.4	chr3_49118120_-	-520.00	-520.00	-520.20
CAediting_278213	ENST00000491859.4	chr3_49118013_-	-395.20	-393.30	-395.20
CAediting_278214	ENST00000491859.4	chr3_49118120_-	-393.30	-393.30	-395.20

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Relation with ADAR for USP19

Correlation between ADAR gene expression and RNA editing frequency

Cancer

CAeditomID

position

ADAR1 (p-val)

ADAR1 (coeff.)

ADAR2 (p-val)

ADAR2 (coeff.)

ADAR3 (p-val)

ADAR3 (coeff.)

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Relation with cancer stages for USP19

Correlation between Cancer stages and RNA editing frequency

Cancer

Stage_type

CAeditomID

position

P-val

Coeff.

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Relation with survival for USP19

Correlation between RNA editing and survival

Cancer

CAeditomID

position

KMpvalue

Coxpvalue

CoxHR

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RelatedDrugs for USP19

Approved drugs targeting this gene.
(DrugBank Version 5.1.8 2021-01-03)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for USP19

Diseases associated with this gene.
(DisGeNet 7.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	RNA A-to-I events
	Differntial gene expression between RNA A-to-I edited tumor samples versus normal samples
	Protein coding region RNA A-to-I editings
	The effects of the RNA editing to the miRNA binding sites
	The effects of the RNA editing to the stability of the RNA structures
	Relation with ADAR
	Relation with cancer stages
	Relation with survival state
	Related drugs with this gene
	Related diseases with this gene