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Editing gene: ALMS1 (CAeditome ID:7840)

Gene summary for ALMS1

Gene summary

Gene information	Gene symbol	ALMS1
	Gene ID	7840
	Gene name	ALMS1 centrosome and basal body associated protein
	Synonyms	ALSS
	Cytomap	2p13.1
	Type of gene	protein-coding
	Description	Alstrom syndrome protein 1Alstrom syndrome 1
	Modification date	20210518
	UniProtAcc	Q8TCU4
	Context

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

Gene	GO ID	GO term	PubMed ID
ALMS1	GO:0005814	Alstrom syndrome protein 1	20844083
ALMS1	GO:0005813	Alstrom syndrome protein 1	15855349
ALMS1	GO:0005813	Alstrom syndrome protein 1	21399614

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RNA A-to-I events for ALMS1

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: ENSG00000116127.16

RNA A-to-I editing events in Cancer.

CAediting_194044(73410377, +), CAediting_194045(73457251, +), CAediting_194046(73457255, +), CAediting_194047(73457268, +), CAediting_194048(73457275, +), CAediting_194049(73457306, +), CAediting_194050(73457312, +), CAediting_194051(73457325, +), CAediting_194052(73457331, +), CAediting_194053(73457332, +), CAediting_194054(73457349, +), CAediting_194055(73457361, +), CAediting_194056(73457371, +), CAediting_194057(73457417, +), CAediting_194058(73457423, +), CAediting_194059(73457426, +), CAediting_194060(73457440, +), CAediting_194061(73457452, +), CAediting_194062(73457478, +), CAediting_194063(73457733, +), CAediting_194064(73457777, +), CAediting_194065(73457795, +), CAediting_194066(73457799, +), CAediting_194067(73457800, +), CAediting_194068(73457813, +), CAediting_194069(73457818, +), CAediting_194070(73457823, +), CAediting_194071(73457826, +), CAediting_194072(73457855, +), CAediting_194073(73457856, +), CAediting_194074(73457857, +), CAediting_194075(73457868, +), CAediting_194076(73457871, +), CAediting_194077(73457872, +), CAediting_194078(73457873, +), CAediting_194079(73457874, +), CAediting_194080(73457875, +), CAediting_194081(73457877, +), CAediting_194082(73457880, +), CAediting_194083(73457881, +), CAediting_194084(73457882, +), CAediting_194085(73457912, +), CAediting_194086(73457913, +), CAediting_194087(73457922, +), CAediting_194088(73457929, +), CAediting_194089(73457930, +), CAediting_194090(73457935, +), CAediting_194091(73457939, +), CAediting_194092(73457942, +), CAediting_194093(73457945, +), CAediting_194094(73457953, +), CAediting_194095(73457954, +), CAediting_194096(73457961, +), CAediting_194097(73457978, +), CAediting_194098(73457984, +), CAediting_194099(73457994, +), CAediting_194100(73458009, +), CAediting_194101(73458016, +), CAediting_194102(73475640, +), CAediting_194103(73491983, +), CAediting_194104(73491995, +), CAediting_194105(73491999, +), CAediting_194106(73492001, +), CAediting_194107(73492013, +), CAediting_194108(73521473, +), CAediting_194109(73521482, +), CAediting_194110(73521503, +), CAediting_194111(73521520, +), CAediting_194112(73521525, +), CAediting_194113(73521558, +), CAediting_194114(73521629, +), CAediting_194115(73521635, +), CAediting_194116(73562197, +), CAediting_194117(73562253, +), CAediting_194118(73562266, +), CAediting_194119(73562278, +), CAediting_194120(73569076, +), CAediting_194121(73582003, +), CAediting_194122(73582004, +), CAediting_194123(73603820, +), CAediting_194124(73605593, +), CAediting_194125(73605728, +), CAediting_194126(73607681, +), CAediting_194127(73607744, +), CAediting_194128(73607773, +), CAediting_194129(73607783, +), CAediting_194130(73607785, +), CAediting_194131(73607847, +), CAediting_194132(73607849, +), CAediting_194133(73607861, +), CAediting_194134(73607886, +), CAediting_194135(73607901, +), CAediting_194136(73607905, +), CAediting_194137(73607914, +), CAediting_194138(73607924, +),

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RNA editing positional annotations for ALMS1 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_194044	chr2_73410377_+	intronic
CAediting_194045	chr2_73457251_+	ncRNA_exonic
CAediting_194046	chr2_73457255_+	ncRNA_exonic
CAediting_194047	chr2_73457268_+	ncRNA_exonic
CAediting_194048	chr2_73457275_+	ncRNA_exonic
CAediting_194049	chr2_73457306_+	ncRNA_exonic
CAediting_194050	chr2_73457312_+	ncRNA_exonic
CAediting_194051	chr2_73457325_+	ncRNA_exonic
CAediting_194052	chr2_73457331_+	ncRNA_intronic
CAediting_194053	chr2_73457332_+	ncRNA_intronic
CAediting_194054	chr2_73457349_+	ncRNA_intronic
CAediting_194055	chr2_73457361_+	ncRNA_intronic
CAediting_194056	chr2_73457371_+	ncRNA_intronic
CAediting_194057	chr2_73457417_+	ncRNA_intronic
CAediting_194058	chr2_73457423_+	ncRNA_intronic
CAediting_194059	chr2_73457426_+	ncRNA_intronic
CAediting_194060	chr2_73457440_+	ncRNA_intronic
CAediting_194061	chr2_73457452_+	ncRNA_intronic
CAediting_194062	chr2_73457478_+	ncRNA_intronic
CAediting_194063	chr2_73457733_+	ncRNA_intronic
CAediting_194064	chr2_73457777_+	ncRNA_intronic
CAediting_194065	chr2_73457795_+	ncRNA_intronic
CAediting_194066	chr2_73457799_+	ncRNA_intronic
CAediting_194067	chr2_73457800_+	ncRNA_intronic
CAediting_194068	chr2_73457813_+	ncRNA_intronic
CAediting_194069	chr2_73457818_+	ncRNA_intronic
CAediting_194070	chr2_73457823_+	ncRNA_intronic
CAediting_194071	chr2_73457826_+	ncRNA_intronic
CAediting_194072	chr2_73457855_+	ncRNA_intronic
CAediting_194073	chr2_73457856_+	ncRNA_intronic
CAediting_194074	chr2_73457857_+	ncRNA_intronic
CAediting_194075	chr2_73457868_+	ncRNA_intronic
CAediting_194076	chr2_73457871_+	ncRNA_intronic
CAediting_194077	chr2_73457872_+	ncRNA_intronic
CAediting_194078	chr2_73457873_+	ncRNA_intronic
CAediting_194079	chr2_73457874_+	ncRNA_intronic
CAediting_194080	chr2_73457875_+	ncRNA_intronic
CAediting_194081	chr2_73457877_+	ncRNA_intronic
CAediting_194082	chr2_73457880_+	ncRNA_intronic
CAediting_194083	chr2_73457881_+	ncRNA_intronic
CAediting_194084	chr2_73457882_+	ncRNA_intronic
CAediting_194085	chr2_73457912_+	ncRNA_intronic
CAediting_194086	chr2_73457913_+	ncRNA_intronic
CAediting_194087	chr2_73457922_+	ncRNA_intronic
CAediting_194088	chr2_73457929_+	ncRNA_intronic
CAediting_194089	chr2_73457930_+	ncRNA_intronic
CAediting_194090	chr2_73457935_+	ncRNA_intronic
CAediting_194091	chr2_73457939_+	ncRNA_splicing
CAediting_194092	chr2_73457942_+	ncRNA_exonic
CAediting_194093	chr2_73457945_+	ncRNA_exonic
CAediting_194094	chr2_73457953_+	ncRNA_exonic
CAediting_194095	chr2_73457954_+	ncRNA_exonic
CAediting_194096	chr2_73457961_+	ncRNA_exonic
CAediting_194097	chr2_73457978_+	ncRNA_exonic
CAediting_194098	chr2_73457984_+	ncRNA_exonic
CAediting_194099	chr2_73457994_+	ncRNA_exonic
CAediting_194100	chr2_73458009_+	ncRNA_exonic
CAediting_194101	chr2_73458016_+	ncRNA_exonic
CAediting_194102	chr2_73475640_+	ncRNA_intronic
CAediting_194103	chr2_73491983_+	ncRNA_intronic
CAediting_194104	chr2_73491995_+	ncRNA_intronic
CAediting_194105	chr2_73491999_+	ncRNA_intronic
CAediting_194106	chr2_73492001_+	ncRNA_intronic
CAediting_194107	chr2_73492013_+	ncRNA_intronic
CAediting_194108	chr2_73521473_+	ncRNA_intronic
CAediting_194109	chr2_73521482_+	ncRNA_intronic
CAediting_194110	chr2_73521503_+	ncRNA_intronic
CAediting_194111	chr2_73521520_+	ncRNA_intronic
CAediting_194112	chr2_73521525_+	ncRNA_intronic
CAediting_194113	chr2_73521558_+	ncRNA_intronic
CAediting_194114	chr2_73521629_+	ncRNA_intronic
CAediting_194115	chr2_73521635_+	ncRNA_intronic
CAediting_194116	chr2_73562197_+	ncRNA_intronic
CAediting_194117	chr2_73562253_+	ncRNA_intronic
CAediting_194118	chr2_73562266_+	ncRNA_intronic
CAediting_194119	chr2_73562278_+	ncRNA_intronic
CAediting_194120	chr2_73569076_+	ncRNA_intronic
CAediting_194121	chr2_73582003_+	ncRNA_intronic
CAediting_194122	chr2_73582004_+	ncRNA_intronic
CAediting_194123	chr2_73603820_+	ncRNA_exonic
CAediting_194124	chr2_73605593_+	ncRNA_intronic
CAediting_194125	chr2_73605728_+	ncRNA_intronic
CAediting_194126	chr2_73607681_+	ncRNA_intronic
CAediting_194127	chr2_73607744_+	ncRNA_intronic
CAediting_194128	chr2_73607773_+	ncRNA_intronic
CAediting_194129	chr2_73607783_+	ncRNA_intronic
CAediting_194130	chr2_73607785_+	ncRNA_intronic
CAediting_194131	chr2_73607847_+	ncRNA_intronic
CAediting_194132	chr2_73607849_+	ncRNA_intronic
CAediting_194133	chr2_73607861_+	ncRNA_intronic
CAediting_194134	chr2_73607886_+	ncRNA_intronic
CAediting_194135	chr2_73607901_+	ncRNA_intronic
CAediting_194136	chr2_73607905_+	ncRNA_intronic
CAediting_194137	chr2_73607914_+	ncRNA_intronic
CAediting_194138	chr2_73607924_+	ncRNA_intronic

Repat-regional RNA editing(s).

CAeditome ID	Position	Repeat family	Repeat sub family	Repeat name
CAediting_194044	chr2_73410377_+	SINE	Alu	AluSx
CAediting_194045	chr2_73457251_+	SINE	Alu	AluSz
CAediting_194046	chr2_73457255_+	SINE	Alu	AluSz
CAediting_194047	chr2_73457268_+	SINE	Alu	AluSz
CAediting_194048	chr2_73457275_+	SINE	Alu	AluSz
CAediting_194049	chr2_73457306_+	SINE	Alu	AluSz
CAediting_194050	chr2_73457312_+	SINE	Alu	AluSz
CAediting_194051	chr2_73457325_+	SINE	Alu	AluSz
CAediting_194052	chr2_73457331_+	SINE	Alu	AluSz
CAediting_194053	chr2_73457332_+	SINE	Alu	AluSz
CAediting_194054	chr2_73457349_+	SINE	Alu	AluSz
CAediting_194055	chr2_73457361_+	SINE	Alu	AluSz
CAediting_194056	chr2_73457371_+	SINE	Alu	AluSz
CAediting_194057	chr2_73457417_+	SINE	Alu	AluSz
CAediting_194058	chr2_73457423_+	SINE	Alu	AluSz
CAediting_194059	chr2_73457426_+	SINE	Alu	AluSz
CAediting_194060	chr2_73457440_+	SINE	Alu	AluSz
CAediting_194061	chr2_73457452_+	SINE	Alu	AluSz
CAediting_194062	chr2_73457478_+	SINE	Alu	AluSz
CAediting_194063	chr2_73457733_+	LINE	CR1	L3
CAediting_194064	chr2_73457777_+	SINE	Alu	AluSz
CAediting_194065	chr2_73457795_+	SINE	Alu	AluSz
CAediting_194066	chr2_73457799_+	SINE	Alu	AluSz
CAediting_194067	chr2_73457800_+	SINE	Alu	AluSz
CAediting_194068	chr2_73457813_+	SINE	Alu	AluSz
CAediting_194069	chr2_73457818_+	SINE	Alu	AluSz
CAediting_194070	chr2_73457823_+	SINE	Alu	AluSz
CAediting_194071	chr2_73457826_+	SINE	Alu	AluSz
CAediting_194072	chr2_73457855_+	SINE	Alu	AluSz
CAediting_194073	chr2_73457856_+	SINE	Alu	AluSz
CAediting_194074	chr2_73457857_+	SINE	Alu	AluSz
CAediting_194075	chr2_73457868_+	SINE	Alu	AluSz
CAediting_194076	chr2_73457871_+	SINE	Alu	AluSz
CAediting_194077	chr2_73457872_+	SINE	Alu	AluSz
CAediting_194078	chr2_73457873_+	SINE	Alu	AluSz
CAediting_194079	chr2_73457874_+	SINE	Alu	AluSz
CAediting_194080	chr2_73457875_+	SINE	Alu	AluSz
CAediting_194081	chr2_73457877_+	SINE	Alu	AluSz
CAediting_194082	chr2_73457880_+	SINE	Alu	AluSz
CAediting_194083	chr2_73457881_+	SINE	Alu	AluSz
CAediting_194084	chr2_73457882_+	SINE	Alu	AluSz
CAediting_194085	chr2_73457912_+	SINE	Alu	AluSz
CAediting_194086	chr2_73457913_+	SINE	Alu	AluSz
CAediting_194087	chr2_73457922_+	SINE	Alu	AluSz
CAediting_194088	chr2_73457929_+	SINE	Alu	AluSz
CAediting_194089	chr2_73457930_+	SINE	Alu	AluSz
CAediting_194090	chr2_73457935_+	SINE	Alu	AluSz
CAediting_194091	chr2_73457939_+	SINE	Alu	AluSz
CAediting_194092	chr2_73457942_+	SINE	Alu	AluSz
CAediting_194093	chr2_73457945_+	SINE	Alu	AluSz
CAediting_194094	chr2_73457953_+	SINE	Alu	AluSz
CAediting_194095	chr2_73457954_+	SINE	Alu	AluSz
CAediting_194096	chr2_73457961_+	SINE	Alu	AluSz
CAediting_194097	chr2_73457978_+	SINE	Alu	AluSz
CAediting_194098	chr2_73457984_+	SINE	Alu	AluSz
CAediting_194099	chr2_73457994_+	SINE	Alu	AluSz
CAediting_194100	chr2_73458009_+	SINE	Alu	AluSz
CAediting_194101	chr2_73458016_+	SINE	Alu	AluSz
CAediting_194102	chr2_73475640_+	LINE	L1	L1MB8
CAediting_194103	chr2_73491983_+	LINE	L1	L1MC4a
CAediting_194104	chr2_73491995_+	LINE	L1	L1MC4a
CAediting_194105	chr2_73491999_+	LINE	L1	L1MC4a
CAediting_194106	chr2_73492001_+	LINE	L1	L1MC4a
CAediting_194107	chr2_73492013_+	LINE	L1	L1MC4a
CAediting_194108	chr2_73521473_+	SINE	Alu	AluY
CAediting_194109	chr2_73521482_+	SINE	Alu	AluY
CAediting_194110	chr2_73521503_+	SINE	Alu	AluY
CAediting_194111	chr2_73521520_+	SINE	Alu	AluY
CAediting_194112	chr2_73521525_+	SINE	Alu	AluY
CAediting_194113	chr2_73521558_+	SINE	Alu	AluY
CAediting_194114	chr2_73521629_+	SINE	Alu	AluY
CAediting_194115	chr2_73521635_+	SINE	Alu	AluY
CAediting_194116	chr2_73562197_+	SINE	Alu	FRAM
CAediting_194117	chr2_73562253_+	SINE	Alu	FRAM
CAediting_194118	chr2_73562266_+	SINE	Alu	FRAM
CAediting_194119	chr2_73562278_+	SINE	Alu	FRAM
CAediting_194120	chr2_73569076_+	SINE	Alu	AluSz
CAediting_194121	chr2_73582003_+	SINE	Alu	AluSx4
CAediting_194122	chr2_73582004_+	SINE	Alu	AluSx4
CAediting_194123	chr2_73603820_+	SINE	Alu	AluSx
CAediting_194124	chr2_73605593_+	SINE	Alu	AluSq
CAediting_194125	chr2_73605728_+	SINE	Alu	AluSq
CAediting_194126	chr2_73607681_+	SINE	Alu	AluSg4
CAediting_194127	chr2_73607744_+	SINE	Alu	AluSg4
CAediting_194128	chr2_73607773_+	SINE	Alu	AluSg4
CAediting_194129	chr2_73607783_+	SINE	Alu	AluSg4
CAediting_194130	chr2_73607785_+	SINE	Alu	AluSg4
CAediting_194131	chr2_73607847_+	SINE	Alu	AluSg4
CAediting_194132	chr2_73607849_+	SINE	Alu	AluSg4
CAediting_194133	chr2_73607861_+	SINE	Alu	AluSg4
CAediting_194134	chr2_73607886_+	SINE	Alu	AluSg4
CAediting_194135	chr2_73607901_+	SINE	Alu	AluSg4
CAediting_194136	chr2_73607905_+	SINE	Alu	AluSg4
CAediting_194137	chr2_73607914_+	SINE	Alu	AluSg4
CAediting_194138	chr2_73607924_+	SINE	Alu	AluSg4

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RNA A-to-I editing events in the alternative splicing sites for ALMS1

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 ENSG00000116127.16.ALMS1.

Correlation between RNA A-to-I editing and PSI for ENSG00000116127.16.ALMS1.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for ALMS1

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 ALMS1

- 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 ALMS1

**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_+	ENSG00000116127.16	ENST00000423048	hsa-miR-605-3p	73573458	73573464	7mer-m8	73573446	73573465	143	-13.98
CAediting_1368054	chr19_46709310_-	ENSG00000116127.16	ENST00000423048	hsa-miR-320e	73550295	73550302	8mer-1a	73550285	73550302	145	-17.8

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_+	ENSG00000116127.16	ENST00000423048	hsa-miR-4804-3p	73573480	73573486	7mer-m8	73573467	73573487	140	-8.07

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for ALMS1

- 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.
ENST00000620466.3	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_194123	ENST00000620466.3	chr2_73603820_+	-1812.70	-1812.90	-1812.70

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Relation with ADAR for ALMS1

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 ALMS1

Correlation between Cancer stages and RNA editing frequency

Cancer

Stage_type

CAeditomID

position

P-val

Coeff.

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Relation with survival for ALMS1

Correlation between RNA editing and survival

Cancer

CAeditomID

position

KMpvalue

Coxpvalue

CoxHR

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RelatedDrugs for ALMS1

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 ALMS1

Diseases associated with this gene.
(DisGeNet 7.0)

Gene	Disease ID	Disease name	# pubmeds	Source
ALMS1	C0268425	Alstrom Syndrome	11	CLINGEN;CTD_human;GENOMICS_ENGLAND
ALMS1	C0007193	Cardiomyopathy, Dilated	1	CTD_human
ALMS1	C0152427	Polydactyly	1	GENOMICS_ENGLAND
ALMS1	C0752166	Bardet-Biedl Syndrome	1	GENOMICS_ENGLAND
ALMS1	C1449563	Cardiomyopathy, Familial Idiopathic	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