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Editing gene: TSEN54 (CAeditome ID:283989)

Gene summary for TSEN54

Gene summary

Gene information	Gene symbol	TSEN54
	Gene ID	283989
	Gene name	tRNA splicing endonuclease subunit 54
	Synonyms	PCH2A\|PCH4\|PCH5\|SEN54L\|sen54
	Cytomap	17q25.1
	Type of gene	protein-coding
	Description	tRNA-splicing endonuclease subunit Sen54SEN54 homologTSEN54 tRNA splicing endonuclease subunithsSen54tRNA-intron endonuclease Sen54
	Modification date	20210518
	UniProtAcc	Q7Z6J9
	Context

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

Gene	GO ID	GO term	PubMed ID
TSEN54	GO:0006388	tRNA-splicing endonuclease subunit Sen54	17495927

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RNA A-to-I events for TSEN54

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: ENSG00000182173.11

RNA A-to-I editing events in Cancer.

CAediting_1236080(75519594, +), CAediting_1236081(75519662, +), CAediting_1236082(75519663, +), CAediting_1236083(75519666, +), CAediting_1236084(75519704, +), CAediting_1236085(75519782, +), CAediting_1236086(75519809, +), CAediting_1236087(75519825, +), CAediting_1236088(75519833, +), CAediting_1236089(75519853, +), CAediting_1236090(75520312, +), CAediting_1236091(75520314, +), CAediting_1236092(75520315, +), CAediting_1236093(75520360, +), CAediting_1236094(75520383, +), CAediting_1236095(75520394, +), CAediting_1236096(75520428, +), CAediting_1236097(75520429, +), CAediting_1236098(75520434, +), CAediting_1236099(75520435, +), CAediting_1236100(75520463, +), CAediting_1236101(75520479, +), CAediting_1236102(75520482, +), CAediting_1236103(75520488, +), CAediting_1236104(75520506, +), CAediting_1236105(75520507, +), CAediting_1236106(75520520, +), CAediting_1236107(75520536, +), CAediting_1236108(75520546, +), CAediting_1236109(75520574, +), CAediting_1236110(75520575, +), CAediting_1236111(75520678, +), CAediting_1236112(75520684, +), CAediting_1236113(75520700, +), CAediting_1236114(75520701, +), CAediting_1236115(75520714, +), CAediting_1236116(75520723, +), CAediting_1236117(75520727, +), CAediting_1236118(75520755, +), CAediting_1236119(75520778, +), CAediting_1236120(75520801, +), CAediting_1236121(75520807, +), CAediting_1236122(75520833, +), CAediting_1236123(75520845, +), CAediting_1236124(75520858, +), CAediting_1236125(75520876, +), CAediting_1236126(75520877, +), CAediting_1236127(75520897, +), CAediting_1236128(75520906, +), CAediting_1236129(75520940, +), CAediting_1236130(75522931, +), CAediting_1236131(75522974, +), CAediting_1236132(75523005, +), CAediting_1236133(75523020, +), CAediting_1236134(75523032, +), CAediting_1236135(75523050, +), CAediting_1236136(75523064, +), CAediting_1236137(75523088, +), CAediting_1236138(75523139, +), CAediting_1236139(75523161, +), CAediting_1236140(75523169, +),

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RNA editing positional annotations for TSEN54 using Annovar

Protein coding RNA editing(s).

CAeditome ID

Position

Variant type

ENST

NTchange

AAchange

SIFT_score

Polyphen2_HVAR_score

PROVEAN_pred

Gene structure information of RNA editing(s).

CAeditome ID	Position	Variant type
CAediting_1236080	chr17_75519594_+	ncRNA_intronic
CAediting_1236081	chr17_75519662_+	ncRNA_intronic
CAediting_1236082	chr17_75519663_+	ncRNA_intronic
CAediting_1236083	chr17_75519666_+	ncRNA_intronic
CAediting_1236084	chr17_75519704_+	ncRNA_intronic
CAediting_1236085	chr17_75519782_+	ncRNA_intronic
CAediting_1236086	chr17_75519809_+	ncRNA_intronic
CAediting_1236087	chr17_75519825_+	ncRNA_intronic
CAediting_1236088	chr17_75519833_+	ncRNA_intronic
CAediting_1236089	chr17_75519853_+	ncRNA_intronic
CAediting_1236090	chr17_75520312_+	ncRNA_intronic
CAediting_1236091	chr17_75520314_+	ncRNA_intronic
CAediting_1236092	chr17_75520315_+	ncRNA_intronic
CAediting_1236093	chr17_75520360_+	ncRNA_intronic
CAediting_1236094	chr17_75520383_+	ncRNA_intronic
CAediting_1236095	chr17_75520394_+	ncRNA_intronic
CAediting_1236096	chr17_75520428_+	ncRNA_intronic
CAediting_1236097	chr17_75520429_+	ncRNA_intronic
CAediting_1236098	chr17_75520434_+	ncRNA_intronic
CAediting_1236099	chr17_75520435_+	ncRNA_intronic
CAediting_1236100	chr17_75520463_+	ncRNA_intronic
CAediting_1236101	chr17_75520479_+	ncRNA_intronic
CAediting_1236102	chr17_75520482_+	ncRNA_intronic
CAediting_1236103	chr17_75520488_+	ncRNA_intronic
CAediting_1236104	chr17_75520506_+	ncRNA_intronic
CAediting_1236105	chr17_75520507_+	ncRNA_intronic
CAediting_1236106	chr17_75520520_+	ncRNA_intronic
CAediting_1236107	chr17_75520536_+	ncRNA_intronic
CAediting_1236108	chr17_75520546_+	ncRNA_intronic
CAediting_1236109	chr17_75520574_+	ncRNA_intronic
CAediting_1236110	chr17_75520575_+	ncRNA_intronic
CAediting_1236111	chr17_75520678_+	ncRNA_intronic
CAediting_1236112	chr17_75520684_+	ncRNA_intronic
CAediting_1236113	chr17_75520700_+	ncRNA_intronic
CAediting_1236114	chr17_75520701_+	ncRNA_intronic
CAediting_1236115	chr17_75520714_+	ncRNA_intronic
CAediting_1236116	chr17_75520723_+	ncRNA_intronic
CAediting_1236117	chr17_75520727_+	ncRNA_intronic
CAediting_1236118	chr17_75520755_+	ncRNA_intronic
CAediting_1236119	chr17_75520778_+	ncRNA_intronic
CAediting_1236120	chr17_75520801_+	ncRNA_intronic
CAediting_1236121	chr17_75520807_+	ncRNA_intronic
CAediting_1236122	chr17_75520833_+	ncRNA_intronic
CAediting_1236123	chr17_75520845_+	ncRNA_intronic
CAediting_1236124	chr17_75520858_+	ncRNA_intronic
CAediting_1236125	chr17_75520876_+	ncRNA_intronic
CAediting_1236126	chr17_75520877_+	ncRNA_intronic
CAediting_1236127	chr17_75520897_+	ncRNA_intronic
CAediting_1236128	chr17_75520906_+	ncRNA_intronic
CAediting_1236129	chr17_75520940_+	ncRNA_intronic
CAediting_1236130	chr17_75522931_+	ncRNA_exonic
CAediting_1236131	chr17_75522974_+	ncRNA_exonic
CAediting_1236132	chr17_75523005_+	ncRNA_exonic
CAediting_1236133	chr17_75523020_+	ncRNA_exonic
CAediting_1236134	chr17_75523032_+	ncRNA_exonic
CAediting_1236135	chr17_75523050_+	ncRNA_exonic
CAediting_1236136	chr17_75523064_+	ncRNA_exonic
CAediting_1236137	chr17_75523088_+	ncRNA_exonic
CAediting_1236138	chr17_75523139_+	ncRNA_exonic
CAediting_1236139	chr17_75523161_+	ncRNA_exonic
CAediting_1236140	chr17_75523169_+	ncRNA_exonic

Repat-regional RNA editing(s).

CAeditome ID	Position	Repeat family	Repeat sub family	Repeat name
CAediting_1236080	chr17_75519594_+	SINE	Alu	AluSz
CAediting_1236081	chr17_75519662_+	SINE	Alu	AluSz
CAediting_1236082	chr17_75519663_+	SINE	Alu	AluSz
CAediting_1236083	chr17_75519666_+	SINE	Alu	AluSz
CAediting_1236084	chr17_75519704_+	SINE	Alu	AluSz
CAediting_1236085	chr17_75519782_+	SINE	Alu	AluSz
CAediting_1236086	chr17_75519809_+	SINE	Alu	AluSz
CAediting_1236087	chr17_75519825_+	SINE	Alu	AluSz
CAediting_1236088	chr17_75519833_+	SINE	Alu	AluSz
CAediting_1236089	chr17_75519853_+	SINE	Alu	AluSz
CAediting_1236090	chr17_75520312_+	SINE	Alu	AluSq2
CAediting_1236091	chr17_75520314_+	SINE	Alu	AluSq2
CAediting_1236092	chr17_75520315_+	SINE	Alu	AluSq2
CAediting_1236093	chr17_75520360_+	SINE	Alu	AluSq2
CAediting_1236094	chr17_75520383_+	SINE	Alu	AluSq2
CAediting_1236095	chr17_75520394_+	SINE	Alu	AluSq2
CAediting_1236096	chr17_75520428_+	SINE	Alu	AluSq2
CAediting_1236097	chr17_75520429_+	SINE	Alu	AluSq2
CAediting_1236098	chr17_75520434_+	SINE	Alu	AluSq2
CAediting_1236099	chr17_75520435_+	SINE	Alu	AluSq2
CAediting_1236100	chr17_75520463_+	SINE	Alu	AluSq2
CAediting_1236101	chr17_75520479_+	SINE	Alu	AluSq2
CAediting_1236102	chr17_75520482_+	SINE	Alu	AluSq2
CAediting_1236103	chr17_75520488_+	SINE	Alu	AluSq2
CAediting_1236104	chr17_75520506_+	SINE	Alu	AluSq2
CAediting_1236105	chr17_75520507_+	SINE	Alu	AluSq2
CAediting_1236106	chr17_75520520_+	SINE	Alu	AluSq2
CAediting_1236107	chr17_75520536_+	SINE	Alu	AluSq2
CAediting_1236108	chr17_75520546_+	SINE	Alu	AluSq2
CAediting_1236109	chr17_75520574_+	SINE	Alu	AluSq2
CAediting_1236110	chr17_75520575_+	SINE	Alu	AluSq2
CAediting_1236111	chr17_75520678_+	SINE	Alu	AluSc
CAediting_1236112	chr17_75520684_+	SINE	Alu	AluSc
CAediting_1236113	chr17_75520700_+	SINE	Alu	AluSc
CAediting_1236114	chr17_75520701_+	SINE	Alu	AluSc
CAediting_1236115	chr17_75520714_+	SINE	Alu	AluSc
CAediting_1236116	chr17_75520723_+	SINE	Alu	AluSc
CAediting_1236117	chr17_75520727_+	SINE	Alu	AluSc
CAediting_1236118	chr17_75520755_+	SINE	Alu	AluSc
CAediting_1236119	chr17_75520778_+	SINE	Alu	AluSc
CAediting_1236120	chr17_75520801_+	SINE	Alu	AluSc
CAediting_1236121	chr17_75520807_+	SINE	Alu	AluSc
CAediting_1236122	chr17_75520833_+	SINE	Alu	AluSc
CAediting_1236123	chr17_75520845_+	SINE	Alu	AluSc
CAediting_1236124	chr17_75520858_+	SINE	Alu	AluSc
CAediting_1236125	chr17_75520876_+	SINE	Alu	AluSc
CAediting_1236126	chr17_75520877_+	SINE	Alu	AluSc
CAediting_1236127	chr17_75520897_+	SINE	Alu	AluSc
CAediting_1236128	chr17_75520906_+	SINE	Alu	AluSc
CAediting_1236129	chr17_75520940_+	SINE	Alu	AluSc
CAediting_1236130	chr17_75522931_+	SINE	Alu	AluSx
CAediting_1236131	chr17_75522974_+	SINE	Alu	AluSx
CAediting_1236132	chr17_75523005_+	SINE	Alu	AluSx
CAediting_1236133	chr17_75523020_+	SINE	Alu	AluSx
CAediting_1236134	chr17_75523032_+	SINE	Alu	AluSx
CAediting_1236135	chr17_75523050_+	SINE	Alu	AluSx
CAediting_1236136	chr17_75523064_+	SINE	Alu	AluSx
CAediting_1236137	chr17_75523088_+	SINE	Alu	AluSx
CAediting_1236138	chr17_75523139_+	SINE	Alu	AluSx
CAediting_1236139	chr17_75523161_+	SINE	Alu	AluSx
CAediting_1236140	chr17_75523169_+	SINE	Alu	AluSx

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RNA A-to-I editing events in the alternative splicing sites for TSEN54

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
IR	CAediting_1236139	chr17_75523161_+	75523161:75523169	5SS	3+0i	AGAGTGAGA	2.37	GGAGTGAGA	0.49
IR	CAediting_1236140	chr17_75523169_+	75523161:75523169	5SS	0+6i	AGAGTGAGA	2.37	AGAGTGAGG	2.6

Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000182173.11.TSEN54.

Correlation between RNA A-to-I editing and PSI for ENSG00000182173.11.TSEN54.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for TSEN54

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 TSEN54

- 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 TSEN54

**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_414656	chr5_72878640_+	ENSG00000182173.11	ENST00000583818	hsa-miR-4804-3p	75521821	75521827	7mer-m8	75521807	75521828	147	-14.58
CAediting_1368054	chr19_46709310_-	ENSG00000182173.11	ENST00000583173	hsa-miR-320e	75522321	75522327	7mer-m8	75522311	75522328	148	-21.48

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
CAediting_1054808	chr15_66496985_-	ENSG00000182173.11	ENST00000583818	hsa-miR-4512	75521724	75521730	7mer-m8	75521710	75521731	140	-19.11

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for TSEN54

- 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.

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

CAeditom_ID

ENST

Editing_Position

MFE_withoneAI

MFE_withoutAI

MFE_withmultipleAI

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Relation with ADAR for TSEN54

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 TSEN54

Correlation between Cancer stages and RNA editing frequency

Cancer

Stage_type

CAeditomID

position

P-val

Coeff.

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Relation with survival for TSEN54

Correlation between RNA editing and survival

Cancer

CAeditomID

position

KMpvalue

Coxpvalue

CoxHR

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RelatedDrugs for TSEN54

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 TSEN54

Diseases associated with this gene.
(DisGeNet 7.0)

Gene	Disease ID	Disease name	# pubmeds	Source
TSEN54	C1848526	Pontocerebellar Hypoplasia Type 2A	4	CTD_human;GENOMICS_ENGLAND;UNIPROT
TSEN54	C1856974	PONTOCEREBELLAR HYPOPLASIA TYPE 4 (disorder)	4	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TSEN54	C1857762	Olivopontocerebellar hypoplasia, fetal-onset	3	GENOMICS_ENGLAND;ORPHANET
TSEN54	C0266468	Congenital pontocerebellar hypoplasia	2	GENOMICS_ENGLAND
TSEN54	C0011168	Deglutition Disorders	1	CTD_human
TSEN54	C0018975	Hemeralopia	1	CTD_human
TSEN54	C0020796	Profound Mental Retardation	1	CTD_human
TSEN54	C0025363	Mental Retardation, Psychosocial	1	CTD_human
TSEN54	C0025958	Microcephaly	1	CTD_human
TSEN54	C0026650	Movement Disorders	1	CTD_human
TSEN54	C0042790	Vision Disorders	1	CTD_human
TSEN54	C0233769	Micropsia	1	CTD_human
TSEN54	C0233771	Macropsia	1	CTD_human
TSEN54	C0266487	Etat Marbre	1	CTD_human
TSEN54	C0267071	Oropharyngeal Dysphagia	1	CTD_human
TSEN54	C0267072	Esophageal Dysphagia	1	CTD_human
TSEN54	C0271185	Metamorphopsia	1	CTD_human
TSEN54	C0917816	Mental deficiency	1	CTD_human
TSEN54	C1843504	Pontocerebellar Hypoplasia Type 1	1	ORPHANET
TSEN54	C1956147	Microlissencephaly	1	CTD_human
TSEN54	C3489704	Vision Disability	1	CTD_human
TSEN54	C3665347	Visual Impairment	1	CTD_human
TSEN54	C3714756	Intellectual Disability	1	CTD_human
TSEN54	C3853041	Severe Congenital Microcephaly	1	CTD_human

	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