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Editing gene: TRAPPC4 (CAeditome ID:51399)

Gene summary for TRAPPC4

Gene summary

Gene information	Gene symbol	TRAPPC4
	Gene ID	51399
	Gene name	trafficking protein particle complex subunit 4
	Synonyms	CGI-104\|HSPC172\|NEDESBA\|PTD009\|SBDN\|SYNBINDIN\|TRS23
	Cytomap	11q23.3
	Type of gene	protein-coding
	Description	trafficking protein particle complex subunit 4TRS23 homologhematopoietic stem/progenitor cell protein 172trafficking protein particle complex 4
	Modification date	20210518
	UniProtAcc	Q9Y296
	Context

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

Gene	GO ID	GO term	PubMed ID
TRAPPC4	GO:0030008	Trafficking protein particle complex subunit 4	21525244

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RNA A-to-I events for TRAPPC4

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: ENSG00000196655.8

RNA A-to-I editing events in Cancer.

CAediting_856196(119020542, +), CAediting_856197(119020560, +), CAediting_856198(119020642, +), CAediting_856199(119021074, +), CAediting_856200(119021118, +), CAediting_856201(119022009, +), CAediting_856202(119022065, +), CAediting_856203(119022084, +), CAediting_856204(119022085, +), CAediting_856205(119022102, +), CAediting_856206(119022111, +), CAediting_856207(119022114, +), CAediting_856208(119022168, +), CAediting_856209(119022169, +), CAediting_856210(119022173, +), CAediting_856211(119022204, +), CAediting_856212(119022206, +), CAediting_856213(119022258, +), CAediting_856214(119022302, +), CAediting_856215(119022314, +), CAediting_856216(119022327, +), CAediting_856217(119022335, +), CAediting_856218(119022336, +), CAediting_856219(119022351, +), CAediting_856220(119022352, +), CAediting_856221(119022358, +), CAediting_856222(119022371, +), CAediting_856223(119022409, +), CAediting_856224(119022423, +), CAediting_856225(119022426, +), CAediting_856226(119022427, +), CAediting_856227(119022430, +), CAediting_856228(119022438, +), CAediting_856229(119022441, +), CAediting_856230(119022467, +), CAediting_856231(119022481, +), CAediting_856232(119022484, +), CAediting_856233(119022485, +), CAediting_856234(119022490, +), CAediting_856235(119022507, +), CAediting_856236(119022508, +), CAediting_856237(119022509, +), CAediting_856238(119022516, +), CAediting_856239(119022534, +), CAediting_856240(119022537, +), CAediting_856241(119022568, +), CAediting_856242(119022575, +), CAediting_856243(119022688, +), CAediting_856244(119022689, +), CAediting_856245(119022694, +), CAediting_856246(119022719, +), CAediting_856247(119022772, +), CAediting_856248(119022778, +), CAediting_856249(119022779, +), CAediting_856250(119022813, +), CAediting_856251(119022833, +), CAediting_856252(119022834, +), CAediting_856253(119022842, +), CAediting_856254(119022846, +), CAediting_856255(119022851, +), CAediting_856256(119023029, +), CAediting_856257(119023032, +), CAediting_856258(119023042, +), CAediting_856259(119023045, +), CAediting_856260(119023064, +), CAediting_856261(119023069, +), CAediting_856262(119023082, +), CAediting_856263(119023094, +), CAediting_856264(119023104, +), CAediting_856265(119023110, +), CAediting_856266(119023145, +), CAediting_856267(119023154, +), CAediting_856268(119023162, +), CAediting_856269(119023174, +), CAediting_856270(119023179, +), CAediting_856271(119023185, +), CAediting_856272(119023186, +), CAediting_856273(119023187, +), CAediting_856274(119023194, +), CAediting_856275(119023199, +),

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RNA editing positional annotations for TRAPPC4 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_856196	chr11_119020542_+	ncRNA_exonic
CAediting_856197	chr11_119020560_+	ncRNA_exonic
CAediting_856198	chr11_119020642_+	ncRNA_exonic
CAediting_856199	chr11_119021074_+	ncRNA_exonic
CAediting_856200	chr11_119021118_+	ncRNA_exonic
CAediting_856201	chr11_119022009_+	ncRNA_intronic
CAediting_856202	chr11_119022065_+	ncRNA_intronic
CAediting_856203	chr11_119022084_+	ncRNA_intronic
CAediting_856204	chr11_119022085_+	ncRNA_intronic
CAediting_856205	chr11_119022102_+	ncRNA_intronic
CAediting_856206	chr11_119022111_+	ncRNA_intronic
CAediting_856207	chr11_119022114_+	ncRNA_intronic
CAediting_856208	chr11_119022168_+	ncRNA_intronic
CAediting_856209	chr11_119022169_+	ncRNA_intronic
CAediting_856210	chr11_119022173_+	ncRNA_intronic
CAediting_856211	chr11_119022204_+	ncRNA_intronic
CAediting_856212	chr11_119022206_+	ncRNA_intronic
CAediting_856213	chr11_119022258_+	ncRNA_intronic
CAediting_856214	chr11_119022302_+	ncRNA_intronic
CAediting_856215	chr11_119022314_+	ncRNA_intronic
CAediting_856216	chr11_119022327_+	ncRNA_intronic
CAediting_856217	chr11_119022335_+	ncRNA_intronic
CAediting_856218	chr11_119022336_+	ncRNA_intronic
CAediting_856219	chr11_119022351_+	ncRNA_intronic
CAediting_856220	chr11_119022352_+	ncRNA_intronic
CAediting_856221	chr11_119022358_+	ncRNA_intronic
CAediting_856222	chr11_119022371_+	ncRNA_intronic
CAediting_856223	chr11_119022409_+	ncRNA_intronic
CAediting_856224	chr11_119022423_+	ncRNA_intronic
CAediting_856225	chr11_119022426_+	ncRNA_intronic
CAediting_856226	chr11_119022427_+	ncRNA_intronic
CAediting_856227	chr11_119022430_+	ncRNA_intronic
CAediting_856228	chr11_119022438_+	ncRNA_intronic
CAediting_856229	chr11_119022441_+	ncRNA_intronic
CAediting_856230	chr11_119022467_+	ncRNA_intronic
CAediting_856231	chr11_119022481_+	ncRNA_intronic
CAediting_856232	chr11_119022484_+	ncRNA_intronic
CAediting_856233	chr11_119022485_+	ncRNA_intronic
CAediting_856234	chr11_119022490_+	ncRNA_intronic
CAediting_856235	chr11_119022507_+	ncRNA_intronic
CAediting_856236	chr11_119022508_+	ncRNA_intronic
CAediting_856237	chr11_119022509_+	ncRNA_intronic
CAediting_856238	chr11_119022516_+	ncRNA_intronic
CAediting_856239	chr11_119022534_+	ncRNA_intronic
CAediting_856240	chr11_119022537_+	ncRNA_intronic
CAediting_856241	chr11_119022568_+	ncRNA_intronic
CAediting_856242	chr11_119022575_+	ncRNA_intronic
CAediting_856243	chr11_119022688_+	ncRNA_intronic
CAediting_856244	chr11_119022689_+	ncRNA_intronic
CAediting_856245	chr11_119022694_+	ncRNA_intronic
CAediting_856246	chr11_119022719_+	ncRNA_intronic
CAediting_856247	chr11_119022772_+	ncRNA_intronic
CAediting_856248	chr11_119022778_+	ncRNA_intronic
CAediting_856249	chr11_119022779_+	ncRNA_intronic
CAediting_856250	chr11_119022813_+	ncRNA_intronic
CAediting_856251	chr11_119022833_+	ncRNA_intronic
CAediting_856252	chr11_119022834_+	ncRNA_intronic
CAediting_856253	chr11_119022842_+	ncRNA_intronic
CAediting_856254	chr11_119022846_+	ncRNA_intronic
CAediting_856255	chr11_119022851_+	ncRNA_intronic
CAediting_856256	chr11_119023029_+	ncRNA_exonic
CAediting_856257	chr11_119023032_+	ncRNA_exonic
CAediting_856258	chr11_119023042_+	ncRNA_exonic
CAediting_856259	chr11_119023045_+	ncRNA_exonic
CAediting_856260	chr11_119023064_+	ncRNA_exonic
CAediting_856261	chr11_119023069_+	ncRNA_exonic
CAediting_856262	chr11_119023082_+	ncRNA_exonic
CAediting_856263	chr11_119023094_+	ncRNA_exonic
CAediting_856264	chr11_119023104_+	ncRNA_exonic
CAediting_856265	chr11_119023110_+	ncRNA_exonic
CAediting_856266	chr11_119023145_+	ncRNA_exonic
CAediting_856267	chr11_119023154_+	ncRNA_exonic
CAediting_856268	chr11_119023162_+	ncRNA_exonic
CAediting_856269	chr11_119023174_+	ncRNA_exonic
CAediting_856270	chr11_119023179_+	ncRNA_exonic
CAediting_856271	chr11_119023185_+	ncRNA_exonic
CAediting_856272	chr11_119023186_+	ncRNA_exonic
CAediting_856273	chr11_119023187_+	ncRNA_exonic
CAediting_856274	chr11_119023194_+	ncRNA_exonic
CAediting_856275	chr11_119023199_+	ncRNA_exonic

Repat-regional RNA editing(s).

CAeditome ID	Position	Repeat family	Repeat sub family	Repeat name
CAediting_856196	chr11_119020542_+	SINE	Alu	AluSp
CAediting_856197	chr11_119020560_+	SINE	Alu	AluSp
CAediting_856198	chr11_119020642_+	SINE	Alu	AluSp
CAediting_856199	chr11_119021074_+	SINE	Alu	AluSx1
CAediting_856200	chr11_119021118_+	SINE	Alu	AluSx1
CAediting_856201	chr11_119022009_+	SINE	Alu	AluSp
CAediting_856202	chr11_119022065_+	SINE	Alu	AluSp
CAediting_856203	chr11_119022084_+	SINE	Alu	AluSp
CAediting_856204	chr11_119022085_+	SINE	Alu	AluSp
CAediting_856205	chr11_119022102_+	SINE	Alu	AluSp
CAediting_856206	chr11_119022111_+	SINE	Alu	AluSp
CAediting_856207	chr11_119022114_+	SINE	Alu	AluSp
CAediting_856208	chr11_119022168_+	SINE	Alu	AluSp
CAediting_856209	chr11_119022169_+	SINE	Alu	AluSp
CAediting_856210	chr11_119022173_+	SINE	Alu	AluSp
CAediting_856211	chr11_119022204_+	SINE	Alu	AluSp
CAediting_856212	chr11_119022206_+	SINE	Alu	AluSp
CAediting_856213	chr11_119022258_+	SINE	Alu	AluSp
CAediting_856216	chr11_119022327_+	SINE	Alu	AluJb
CAediting_856217	chr11_119022335_+	SINE	Alu	AluJb
CAediting_856218	chr11_119022336_+	SINE	Alu	AluJb
CAediting_856219	chr11_119022351_+	SINE	Alu	AluJb
CAediting_856220	chr11_119022352_+	SINE	Alu	AluJb
CAediting_856221	chr11_119022358_+	SINE	Alu	AluJb
CAediting_856222	chr11_119022371_+	SINE	Alu	AluJb
CAediting_856223	chr11_119022409_+	SINE	Alu	AluJb
CAediting_856224	chr11_119022423_+	SINE	Alu	AluJb
CAediting_856225	chr11_119022426_+	SINE	Alu	AluJb
CAediting_856226	chr11_119022427_+	SINE	Alu	AluJb
CAediting_856227	chr11_119022430_+	SINE	Alu	AluJb
CAediting_856228	chr11_119022438_+	SINE	Alu	AluJb
CAediting_856229	chr11_119022441_+	SINE	Alu	AluJb
CAediting_856230	chr11_119022467_+	SINE	Alu	AluJb
CAediting_856231	chr11_119022481_+	SINE	Alu	AluJb
CAediting_856232	chr11_119022484_+	SINE	Alu	AluJb
CAediting_856233	chr11_119022485_+	SINE	Alu	AluJb
CAediting_856234	chr11_119022490_+	SINE	Alu	AluJb
CAediting_856235	chr11_119022507_+	SINE	Alu	AluJb
CAediting_856236	chr11_119022508_+	SINE	Alu	AluJb
CAediting_856237	chr11_119022509_+	SINE	Alu	AluJb
CAediting_856238	chr11_119022516_+	SINE	Alu	AluJb
CAediting_856239	chr11_119022534_+	SINE	Alu	AluJb
CAediting_856240	chr11_119022537_+	SINE	Alu	AluJb
CAediting_856241	chr11_119022568_+	SINE	Alu	AluJb
CAediting_856242	chr11_119022575_+	SINE	Alu	AluJb
CAediting_856243	chr11_119022688_+	SINE	Alu	AluSz
CAediting_856244	chr11_119022689_+	SINE	Alu	AluSz
CAediting_856245	chr11_119022694_+	SINE	Alu	AluSz
CAediting_856246	chr11_119022719_+	SINE	Alu	AluSz
CAediting_856247	chr11_119022772_+	SINE	Alu	AluSz
CAediting_856248	chr11_119022778_+	SINE	Alu	AluSz
CAediting_856249	chr11_119022779_+	SINE	Alu	AluSz
CAediting_856250	chr11_119022813_+	SINE	Alu	AluSz
CAediting_856251	chr11_119022833_+	SINE	Alu	AluSz
CAediting_856252	chr11_119022834_+	SINE	Alu	AluSz
CAediting_856253	chr11_119022842_+	SINE	Alu	AluSz
CAediting_856254	chr11_119022846_+	SINE	Alu	AluSz
CAediting_856255	chr11_119022851_+	SINE	Alu	AluSz
CAediting_856256	chr11_119023029_+	SINE	Alu	AluSq2
CAediting_856257	chr11_119023032_+	SINE	Alu	AluSq2
CAediting_856258	chr11_119023042_+	SINE	Alu	AluSq2
CAediting_856259	chr11_119023045_+	SINE	Alu	AluSq2
CAediting_856260	chr11_119023064_+	SINE	Alu	AluSq2
CAediting_856261	chr11_119023069_+	SINE	Alu	AluSq2
CAediting_856262	chr11_119023082_+	SINE	Alu	AluSq2
CAediting_856263	chr11_119023094_+	SINE	Alu	AluSq2
CAediting_856264	chr11_119023104_+	SINE	Alu	AluSq2
CAediting_856265	chr11_119023110_+	SINE	Alu	AluSq2
CAediting_856266	chr11_119023145_+	SINE	Alu	AluSq2
CAediting_856267	chr11_119023154_+	SINE	Alu	AluSq2
CAediting_856268	chr11_119023162_+	SINE	Alu	AluSq2
CAediting_856269	chr11_119023174_+	SINE	Alu	AluSq2
CAediting_856270	chr11_119023179_+	SINE	Alu	AluSq2
CAediting_856271	chr11_119023185_+	SINE	Alu	AluSq2
CAediting_856272	chr11_119023186_+	SINE	Alu	AluSq2
CAediting_856273	chr11_119023187_+	SINE	Alu	AluSq2
CAediting_856274	chr11_119023194_+	SINE	Alu	AluSq2
CAediting_856275	chr11_119023199_+	SINE	Alu	AluSq2

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RNA A-to-I editing events in the alternative splicing sites for TRAPPC4

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

Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000196655.8.TRAPPC4.

Correlation between RNA A-to-I editing and PSI for ENSG00000196655.8.TRAPPC4.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for TRAPPC4

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 TRAPPC4

- 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 TRAPPC4

**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_748296	chr10_51299626_+	ENSG00000196655.8	ENST00000525079	hsa-miR-605-3p	119021844	119021851	8mer-1a	119021828	119021851	146	-17.99
CAediting_748296	chr10_51299626_+	ENSG00000196655.8	ENST00000533012	hsa-miR-605-3p	119021844	119021851	8mer-1a	119021828	119021851	146	-17.99
CAediting_1229414	chr17_67471546_+	ENSG00000196655.8	ENST00000525303	hsa-miR-548aa	119023580	119023587	8mer-1a	119023563	119023587	140	-8.82
CAediting_1229414	chr17_67471546_+	ENSG00000196655.8	ENST00000434101	hsa-miR-548aa	119023580	119023587	8mer-1a	119023563	119023587	140	-8.82
CAediting_1229414	chr17_67471546_+	ENSG00000196655.8	ENST00000359005	hsa-miR-548aa	119023580	119023587	8mer-1a	119023563	119023587	140	-8.82
CAediting_1229414	chr17_67471546_+	ENSG00000196655.8	ENST00000533632	hsa-miR-548aa	119023580	119023587	8mer-1a	119023563	119023587	140	-8.82
CAediting_1399425	chr20_1392958_-	ENSG00000196655.8	ENST00000533058	hsa-miR-6869-5p	119025378	119025384	7mer-m8	119025365	119025385	151	-26.75
CAediting_396018	chr5_1062918_-	ENSG00000196655.8	ENST00000525079	hsa-miR-4635	119021847	119021854	8mer-1a	119021834	119021854	154	-16.28
CAediting_396018	chr5_1062918_-	ENSG00000196655.8	ENST00000533012	hsa-miR-4635	119021847	119021854	8mer-1a	119021834	119021854	154	-16.28
CAediting_1229414	chr17_67471546_+	ENSG00000196655.8	ENST00000533012	hsa-miR-548aa	119023580	119023587	8mer-1a	119023563	119023587	140	-8.82

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_1229414	chr17_67471546_+	ENSG00000196655.8	ENST00000533632	hsa-miR-548aa	119023688	119023694	7mer-m8	119023670	119023695	153	-8.75
CAediting_1229415	chr17_67471547_+	ENSG00000196655.8	ENST00000533632	hsa-miR-548aa	119023688	119023694	7mer-m8	119023670	119023695	153	-8.75
CAediting_1368054	chr19_46709310_-	ENSG00000196655.8	ENST00000533058	hsa-miR-320e	119025119	119025125	7mer-m8	119025109	119025126	148	-14.26

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for TRAPPC4

- 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 TRAPPC4

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 TRAPPC4

Correlation between Cancer stages and RNA editing frequency

Cancer	Stage_type	CAeditomID	position	P-val	Coeff.
KIRC	pathologic_stage	CAediting_856233	chr11_119022485_+	0.0230731833975101	0.202343437543153

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Relation with survival for TRAPPC4

Correlation between RNA editing and survival

Cancer	CAeditomID	position	KMpvalue	Coxpvalue	CoxHR
OV	CAediting_856270	chr11_119023179_+	0.030967474746441	0.0448253	11.343

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RelatedDrugs for TRAPPC4

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 TRAPPC4

Diseases associated with this gene.
(DisGeNet 7.0)

Gene	Disease ID	Disease name	# pubmeds	Source
TRAPPC4	C0036439	Scoliosis, unspecified	1	GENOMICS_ENGLAND
TRAPPC4	C0036572	Seizures	1	GENOMICS_ENGLAND
TRAPPC4	C0232466	Feeding difficulties	1	GENOMICS_ENGLAND
TRAPPC4	C0234398	Visual Cortex Disorder	1	GENOMICS_ENGLAND
TRAPPC4	C0575059	Spastic tetraparesis	1	GENOMICS_ENGLAND
TRAPPC4	C1384666	hearing impairment	1	GENOMICS_ENGLAND
TRAPPC4	C1850456	Progressive microcephaly	1	GENOMICS_ENGLAND
TRAPPC4	C3714756	Intellectual Disability	1	GENOMICS_ENGLAND
TRAPPC4	C4025871	Abnormality of the face	1	GENOMICS_ENGLAND
TRAPPC4	C4048268	Cortical visual impairment	1	GENOMICS_ENGLAND

	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