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Editing gene: COL6A3 (CAeditome ID:1293)

Gene summary for COL6A3

Gene summary

Gene information	Gene symbol	COL6A3
	Gene ID	1293
	Gene name	collagen type VI alpha 3 chain
	Synonyms	BTHLM1\|DYT27\|UCMD1
	Cytomap	2q37.3
	Type of gene	protein-coding
	Description	collagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3epididymis secretory sperm binding protein
	Modification date	20210518
	UniProtAcc	P12111
	Context

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

Gene	GO ID	GO term	PubMed ID
COL6A3	GO:0031012	Collagen alpha-3(VI) chain	18400749

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RNA A-to-I events for COL6A3

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: ENSG00000163359.14

RNA A-to-I editing events in Cancer.

CAediting_250836(237331571, -), CAediting_250837(237343507, -), CAediting_250838(237343511, -), CAediting_250839(237369838, -), CAediting_250840(237369870, -), CAediting_250841(237369885, -), CAediting_250842(237369895, -), CAediting_250843(237369921, -), CAediting_250844(237369922, -), CAediting_250845(237369935, -), CAediting_250846(237369953, -), CAediting_250847(237369954, -), CAediting_250848(237369969, -), CAediting_250849(237369975, -), CAediting_250850(237369993, -), CAediting_250851(237369997, -), CAediting_250852(237370061, -), CAediting_250853(237370080, -), CAediting_250854(237370081, -), CAediting_250855(237370089, -), CAediting_250856(237370099, -), CAediting_250857(237370105, -), CAediting_250858(237371393, -), CAediting_250859(237371482, -), CAediting_250860(237371545, -), CAediting_250861(237382126, -), CAediting_250862(237382138, -), CAediting_250863(237382139, -), CAediting_250864(237382191, -), CAediting_250865(237382217, -), CAediting_250866(237382220, -), CAediting_250867(237382234, -), CAediting_250868(237382259, -), CAediting_250869(237382261, -), CAediting_250870(237382271, -), CAediting_250871(237382283, -), CAediting_250872(237382296, -), CAediting_250873(237382300, -), CAediting_250874(237382301, -), CAediting_250875(237382307, -), CAediting_250876(237382320, -), CAediting_250877(237382369, -), CAediting_250878(237382374, -), CAediting_250879(237382375, -), CAediting_250880(237382376, -), CAediting_250881(237382817, -), CAediting_250882(237382850, -), CAediting_250883(237382880, -), CAediting_250884(237382884, -), CAediting_250885(237382885, -), CAediting_250886(237382893, -), CAediting_250887(237382896, -), CAediting_250888(237382916, -), CAediting_250889(237382920, -), CAediting_250890(237382925, -), CAediting_250891(237382926, -), CAediting_250892(237382952, -), CAediting_250893(237382956, -), CAediting_250894(237382957, -), CAediting_250895(237382958, -), CAediting_250896(237382981, -), CAediting_250897(237382992, -), CAediting_250898(237382993, -), CAediting_250899(237383000, -), CAediting_250900(237383003, -), CAediting_250901(237383006, -), CAediting_250902(237383012, -), CAediting_250903(237383026, -), CAediting_250904(237383063, -), CAediting_250905(237383066, -), CAediting_250906(237383071, -), CAediting_250907(237383072, -), CAediting_250908(237383080, -), CAediting_250909(237391806, -), CAediting_250910(237406982, -), CAediting_250911(237406983, -), CAediting_250912(237406992, -), CAediting_250913(237406998, -), CAediting_250914(237407002, -), CAediting_250915(237407048, -), CAediting_250916(237407074, -), CAediting_250917(237407111, -), CAediting_250918(237407138, -), CAediting_250919(237407187, -), CAediting_250920(237407201, -), CAediting_250921(237407207, -), CAediting_250922(237410408, -),

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RNA editing positional annotations for COL6A3 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_250836	chr2_237331571_-	ncRNA_intronic
CAediting_250837	chr2_237343507_-	ncRNA_exonic
CAediting_250838	chr2_237343511_-	ncRNA_exonic
CAediting_250839	chr2_237369838_-	intronic
CAediting_250840	chr2_237369870_-	intronic
CAediting_250841	chr2_237369885_-	intronic
CAediting_250842	chr2_237369895_-	intronic
CAediting_250843	chr2_237369921_-	intronic
CAediting_250844	chr2_237369922_-	intronic
CAediting_250845	chr2_237369935_-	intronic
CAediting_250846	chr2_237369953_-	intronic
CAediting_250847	chr2_237369954_-	intronic
CAediting_250848	chr2_237369969_-	intronic
CAediting_250849	chr2_237369975_-	intronic
CAediting_250850	chr2_237369993_-	intronic
CAediting_250851	chr2_237369997_-	intronic
CAediting_250852	chr2_237370061_-	intronic
CAediting_250853	chr2_237370080_-	intronic
CAediting_250854	chr2_237370081_-	intronic
CAediting_250855	chr2_237370089_-	intronic
CAediting_250856	chr2_237370099_-	intronic
CAediting_250857	chr2_237370105_-	intronic
CAediting_250858	chr2_237371393_-	intronic
CAediting_250859	chr2_237371482_-	intronic
CAediting_250860	chr2_237371545_-	intronic
CAediting_250861	chr2_237382126_-	intronic
CAediting_250862	chr2_237382138_-	intronic
CAediting_250863	chr2_237382139_-	intronic
CAediting_250864	chr2_237382191_-	intronic
CAediting_250865	chr2_237382217_-	intronic
CAediting_250866	chr2_237382220_-	intronic
CAediting_250867	chr2_237382234_-	intronic
CAediting_250868	chr2_237382259_-	intronic
CAediting_250869	chr2_237382261_-	intronic
CAediting_250870	chr2_237382271_-	intronic
CAediting_250871	chr2_237382283_-	intronic
CAediting_250872	chr2_237382296_-	intronic
CAediting_250873	chr2_237382300_-	intronic
CAediting_250874	chr2_237382301_-	intronic
CAediting_250875	chr2_237382307_-	intronic
CAediting_250876	chr2_237382320_-	intronic
CAediting_250877	chr2_237382369_-	intronic
CAediting_250878	chr2_237382374_-	intronic
CAediting_250879	chr2_237382375_-	intronic
CAediting_250880	chr2_237382376_-	intronic
CAediting_250881	chr2_237382817_-	intronic
CAediting_250882	chr2_237382850_-	intronic
CAediting_250883	chr2_237382880_-	intronic
CAediting_250884	chr2_237382884_-	intronic
CAediting_250885	chr2_237382885_-	intronic
CAediting_250886	chr2_237382893_-	intronic
CAediting_250887	chr2_237382896_-	intronic
CAediting_250888	chr2_237382916_-	intronic
CAediting_250889	chr2_237382920_-	intronic
CAediting_250890	chr2_237382925_-	intronic
CAediting_250891	chr2_237382926_-	intronic
CAediting_250892	chr2_237382952_-	intronic
CAediting_250893	chr2_237382956_-	intronic
CAediting_250894	chr2_237382957_-	intronic
CAediting_250895	chr2_237382958_-	intronic
CAediting_250896	chr2_237382981_-	intronic
CAediting_250897	chr2_237382992_-	intronic
CAediting_250898	chr2_237382993_-	intronic
CAediting_250899	chr2_237383000_-	intronic
CAediting_250900	chr2_237383003_-	intronic
CAediting_250901	chr2_237383006_-	intronic
CAediting_250902	chr2_237383012_-	intronic
CAediting_250903	chr2_237383026_-	intronic
CAediting_250904	chr2_237383063_-	intronic
CAediting_250905	chr2_237383066_-	intronic
CAediting_250906	chr2_237383071_-	intronic
CAediting_250907	chr2_237383072_-	intronic
CAediting_250908	chr2_237383080_-	intronic
CAediting_250909	chr2_237391806_-	intronic
CAediting_250910	chr2_237406982_-	intronic
CAediting_250911	chr2_237406983_-	intronic
CAediting_250912	chr2_237406992_-	intronic
CAediting_250913	chr2_237406998_-	intronic
CAediting_250914	chr2_237407002_-	intronic
CAediting_250915	chr2_237407048_-	intronic
CAediting_250916	chr2_237407074_-	intronic
CAediting_250917	chr2_237407111_-	intronic
CAediting_250918	chr2_237407138_-	intronic
CAediting_250919	chr2_237407187_-	intronic
CAediting_250920	chr2_237407201_-	intronic
CAediting_250921	chr2_237407207_-	intronic
CAediting_250922	chr2_237410408_-	intronic

Repat-regional RNA editing(s).

CAeditome ID	Position	Repeat family	Repeat sub family	Repeat name
CAediting_250836	chr2_237331571_-	DNA	TcMar-Mariner	MADE1
CAediting_250837	chr2_237343507_-	SINE	Alu	AluSg
CAediting_250838	chr2_237343511_-	SINE	Alu	AluSg
CAediting_250839	chr2_237369838_-	SINE	Alu	AluJb
CAediting_250840	chr2_237369870_-	SINE	Alu	AluJb
CAediting_250841	chr2_237369885_-	SINE	Alu	AluJb
CAediting_250842	chr2_237369895_-	SINE	Alu	AluJb
CAediting_250843	chr2_237369921_-	SINE	Alu	AluJb
CAediting_250844	chr2_237369922_-	SINE	Alu	AluJb
CAediting_250845	chr2_237369935_-	SINE	Alu	AluJb
CAediting_250846	chr2_237369953_-	SINE	Alu	AluJb
CAediting_250847	chr2_237369954_-	SINE	Alu	AluJb
CAediting_250848	chr2_237369969_-	SINE	Alu	AluJb
CAediting_250849	chr2_237369975_-	SINE	Alu	AluJb
CAediting_250850	chr2_237369993_-	SINE	Alu	AluJb
CAediting_250851	chr2_237369997_-	SINE	Alu	AluJb
CAediting_250852	chr2_237370061_-	SINE	Alu	AluJb
CAediting_250853	chr2_237370080_-	SINE	Alu	AluJb
CAediting_250854	chr2_237370081_-	SINE	Alu	AluJb
CAediting_250855	chr2_237370089_-	SINE	Alu	AluJb
CAediting_250856	chr2_237370099_-	SINE	Alu	AluJb
CAediting_250857	chr2_237370105_-	SINE	Alu	AluJb
CAediting_250858	chr2_237371393_-	SINE	Alu	AluJb
CAediting_250859	chr2_237371482_-	SINE	Alu	AluJb
CAediting_250860	chr2_237371545_-	SINE	Alu	AluJb
CAediting_250861	chr2_237382126_-	SINE	Alu	AluSx1
CAediting_250862	chr2_237382138_-	SINE	Alu	AluSx1
CAediting_250863	chr2_237382139_-	SINE	Alu	AluSx1
CAediting_250864	chr2_237382191_-	SINE	Alu	AluSx1
CAediting_250865	chr2_237382217_-	SINE	Alu	AluSx1
CAediting_250866	chr2_237382220_-	SINE	Alu	AluSx1
CAediting_250867	chr2_237382234_-	SINE	Alu	AluSx1
CAediting_250868	chr2_237382259_-	SINE	Alu	AluSx1
CAediting_250869	chr2_237382261_-	SINE	Alu	AluSx1
CAediting_250870	chr2_237382271_-	SINE	Alu	AluSx1
CAediting_250871	chr2_237382283_-	SINE	Alu	AluSx1
CAediting_250872	chr2_237382296_-	SINE	Alu	AluSx1
CAediting_250873	chr2_237382300_-	SINE	Alu	AluSx1
CAediting_250874	chr2_237382301_-	SINE	Alu	AluSx1
CAediting_250875	chr2_237382307_-	SINE	Alu	AluSx1
CAediting_250876	chr2_237382320_-	SINE	Alu	AluSx1
CAediting_250877	chr2_237382369_-	SINE	Alu	AluSx1
CAediting_250878	chr2_237382374_-	SINE	Alu	AluSx1
CAediting_250879	chr2_237382375_-	SINE	Alu	AluSx1
CAediting_250880	chr2_237382376_-	SINE	Alu	AluSx1
CAediting_250881	chr2_237382817_-	SINE	Alu	AluSz
CAediting_250882	chr2_237382850_-	SINE	Alu	AluSz
CAediting_250883	chr2_237382880_-	SINE	Alu	AluSz
CAediting_250884	chr2_237382884_-	SINE	Alu	AluSz
CAediting_250885	chr2_237382885_-	SINE	Alu	AluSz
CAediting_250886	chr2_237382893_-	SINE	Alu	AluSz
CAediting_250887	chr2_237382896_-	SINE	Alu	AluSz
CAediting_250888	chr2_237382916_-	SINE	Alu	AluSz
CAediting_250889	chr2_237382920_-	SINE	Alu	AluSz
CAediting_250890	chr2_237382925_-	SINE	Alu	AluSz
CAediting_250891	chr2_237382926_-	SINE	Alu	AluSz
CAediting_250892	chr2_237382952_-	SINE	Alu	AluSz
CAediting_250893	chr2_237382956_-	SINE	Alu	AluSz
CAediting_250894	chr2_237382957_-	SINE	Alu	AluSz
CAediting_250895	chr2_237382958_-	SINE	Alu	AluSz
CAediting_250896	chr2_237382981_-	SINE	Alu	AluSz
CAediting_250897	chr2_237382992_-	SINE	Alu	AluSz
CAediting_250898	chr2_237382993_-	SINE	Alu	AluSz
CAediting_250899	chr2_237383000_-	SINE	Alu	AluSz
CAediting_250900	chr2_237383003_-	SINE	Alu	AluSz
CAediting_250901	chr2_237383006_-	SINE	Alu	AluSz
CAediting_250902	chr2_237383012_-	SINE	Alu	AluSz
CAediting_250903	chr2_237383026_-	SINE	Alu	AluSz
CAediting_250904	chr2_237383063_-	SINE	Alu	AluSz
CAediting_250905	chr2_237383066_-	SINE	Alu	AluSz
CAediting_250906	chr2_237383071_-	SINE	Alu	AluSz
CAediting_250907	chr2_237383072_-	SINE	Alu	AluSz
CAediting_250908	chr2_237383080_-	SINE	Alu	AluSz
CAediting_250909	chr2_237391806_-	SINE	Alu	AluSq2
CAediting_250910	chr2_237406982_-	SINE	Alu	AluJo
CAediting_250911	chr2_237406983_-	SINE	Alu	AluJo
CAediting_250912	chr2_237406992_-	SINE	Alu	AluJo
CAediting_250913	chr2_237406998_-	SINE	Alu	AluJo
CAediting_250914	chr2_237407002_-	SINE	Alu	AluJo
CAediting_250915	chr2_237407048_-	SINE	Alu	AluJo
CAediting_250916	chr2_237407074_-	SINE	Alu	AluJo
CAediting_250917	chr2_237407111_-	SINE	Alu	AluJo
CAediting_250918	chr2_237407138_-	SINE	Alu	AluJo
CAediting_250919	chr2_237407187_-	SINE	Alu	AluJo
CAediting_250920	chr2_237407201_-	SINE	Alu	AluJo
CAediting_250921	chr2_237407207_-	SINE	Alu	AluJo
CAediting_250922	chr2_237410408_-	SINE	Alu	AluJb

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RNA A-to-I editing events in the alternative splicing sites for COL6A3

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 ENSG00000163359.14.COL6A3.

Correlation between RNA A-to-I editing and PSI for ENSG00000163359.14.COL6A3.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for COL6A3

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 COL6A3

- 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 COL6A3

**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

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_414656	chr5_72878640_+	ENSG00000163359.14	ENST00000353578	hsa-miR-4804-3p	237324365	237324372	8mer-1a	237324365	237324385	140	-9.79
CAediting_414656	chr5_72878640_+	ENSG00000163359.14	ENST00000472056	hsa-miR-4804-3p	237324365	237324372	8mer-1a	237324365	237324385	140	-9.79
CAediting_414656	chr5_72878640_+	ENSG00000163359.14	ENST00000347401	hsa-miR-4804-3p	237324365	237324372	8mer-1a	237324365	237324385	140	-9.79

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for COL6A3

- 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.
ENST00000491769.1	retained_intron

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_250837	ENST00000491769.1	chr2_237343507_-	-2269.00	-2269.90	-2268.40
CAediting_250838	ENST00000491769.1	chr2_237343511_-	-2269.30	-2269.90	-2268.40

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Relation with ADAR for COL6A3

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.)
STAD	CAediting_250837	chr2_237343507_-	.	.	.	.	1.75846198518035e-05	0.415039931327104

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Relation with cancer stages for COL6A3

Correlation between Cancer stages and RNA editing frequency

Cancer

Stage_type

CAeditomID

position

P-val

Coeff.

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Relation with survival for COL6A3

Correlation between RNA editing and survival

Cancer

CAeditomID

position

KMpvalue

Coxpvalue

CoxHR

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RelatedDrugs for COL6A3

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 COL6A3

Diseases associated with this gene.
(DisGeNet 7.0)

Gene	Disease ID	Disease name	# pubmeds	Source
COL6A3	C1834674	BETHLEM MYOPATHY 1	5	CTD_human;GENOMICS_ENGLAND;UNIPROT
COL6A3	C0410179	Ullrich congenital muscular dystrophy 1	4	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
COL6A3	C4225336	DYSTONIA 27	2	GENOMICS_ENGLAND;ORPHANET;UNIPROT
COL6A3	C0000786	Spontaneous abortion	1	CTD_human
COL6A3	C0000822	Abortion, Tubal	1	CTD_human
COL6A3	C0027708	Nephroblastoma	1	CTD_human
COL6A3	C2930471	Bilateral Wilms Tumor	1	CTD_human
COL6A3	C3830362	Early Pregnancy Loss	1	CTD_human
COL6A3	C4552766	Miscarriage	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