ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for HMGA1

Gene summary

Gene information	Gene symbol	HMGA1
	Gene ID	3159
	Gene name	high mobility group AT-hook 1
	Synonyms	HMG-R\|HMGA1A\|HMGIY
	Cytomap	6p21.31
	Type of gene	protein-coding
	Description	high mobility group protein HMG-I/HMG-Yhigh mobility group protein A1high mobility group protein Rhigh-mobility group (nonhistone chromosomal) protein isoforms I and Ynonhistone chromosomal high-mobility group protein HMG-I/HMG-Y
	Modification date	20180523
	UniProtAcc	P17096
	Context	PubMed: HMGA1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene	GO ID	GO term	PubMed ID
HMGA1	GO:0035986	senescence-associated heterochromatin focus assembly	16901784
HMGA1	GO:0090402	oncogene-induced cell senescence	16901784

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Exon skipping events across known transcript of Ensembl for HMGA1 from UCSC genome browser

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Gene isoform structures and expression levels for HMGA1

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for HMGA1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_450653	6	34204655:34204740:34204980:34205094:34208513:34208598	34204980:34205094	ENSG00000137309.15	ENST00000401473.3,ENST00000311487.5,ENST00000395004.3
exon_skip_450687	6	34204980:34205094:34208513:34208659:34210488:34210555	34208513:34208659	ENSG00000137309.15	ENST00000401473.3,ENST00000478214.1
exon_skip_450689	6	34204980:34205094:34208513:34208692:34210488:34210555	34208513:34208692	ENSG00000137309.15	ENST00000311487.5,ENST00000447654.1,ENST00000395004.3
exon_skip_450704	6	34208513:34208659:34210488:34210572:34211244:34211295	34210488:34210572	ENSG00000137309.15	ENST00000401473.3,ENST00000347617.6,ENST00000478214.1,ENST00000374116.3
exon_skip_450705	6	34208513:34208692:34210488:34210572:34211244:34211295	34210488:34210572	ENSG00000137309.15	ENST00000311487.5,ENST00000447654.1
exon_skip_450707	6	34210488:34210572:34211244:34211295:34212607:34212928	34211244:34211295	ENSG00000137309.15	ENST00000401473.3,ENST00000311487.5,ENST00000447654.1,ENST00000347617.6,ENST00000478214.1,ENST00000374116.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for HMGA1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_450653	6	34204655:34204740:34204980:34205094:34208513:34208598	34204980:34205094	ENSG00000137309.15	ENST00000401473.3,ENST00000311487.5,ENST00000395004.3
exon_skip_450687	6	34204980:34205094:34208513:34208659:34210488:34210555	34208513:34208659	ENSG00000137309.15	ENST00000401473.3,ENST00000478214.1
exon_skip_450689	6	34204980:34205094:34208513:34208692:34210488:34210555	34208513:34208692	ENSG00000137309.15	ENST00000311487.5,ENST00000447654.1,ENST00000395004.3
exon_skip_450704	6	34208513:34208659:34210488:34210572:34211244:34211295	34210488:34210572	ENSG00000137309.15	ENST00000347617.6,ENST00000401473.3,ENST00000478214.1,ENST00000374116.3
exon_skip_450705	6	34208513:34208692:34210488:34210572:34211244:34211295	34210488:34210572	ENSG00000137309.15	ENST00000311487.5,ENST00000447654.1
exon_skip_450707	6	34210488:34210572:34211244:34211295:34212607:34212928	34211244:34211295	ENSG00000137309.15	ENST00000347617.6,ENST00000401473.3,ENST00000311487.5,ENST00000447654.1,ENST00000478214.1,ENST00000374116.3

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for HMGA1

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000311487	34208513	34208692	5CDS-5UTR
ENST00000447654	34208513	34208692	5CDS-5UTR
ENST00000311487	34204980	34205094	5UTR-5UTR
ENST00000311487	34210488	34210572	In-frame
ENST00000447654	34210488	34210572	In-frame
ENST00000311487	34211244	34211295	In-frame
ENST00000447654	34211244	34211295	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000311487	34208513	34208692	5CDS-5UTR
ENST00000447654	34208513	34208692	5CDS-5UTR
ENST00000311487	34204980	34205094	5UTR-5UTR
ENST00000311487	34210488	34210572	In-frame
ENST00000447654	34210488	34210572	In-frame
ENST00000311487	34211244	34211295	In-frame
ENST00000447654	34211244	34211295	In-frame

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Infer the effects of exon skipping event on protein functional features for HMGA1

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000311487	1937	107	34210488	34210572	385	468	45	73
ENST00000447654	2176	107	34210488	34210572	625	708	45	73
ENST00000311487	1937	107	34211244	34211295	469	519	73	90
ENST00000447654	2176	107	34211244	34211295	709	759	73	90

Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000311487	1937	107	34210488	34210572	385	468	45	73
ENST00000447654	2176	107	34210488	34210572	625	708	45	73
ENST00000311487	1937	107	34211244	34211295	469	519	73	90
ENST00000447654	2176	107	34211244	34211295	709	759	73	90

Lost protein functional features of individual exon skipping events in TCGA.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P17096	45	73	35	45	Alternative sequence	ID=VSP_002182;Note=In isoform HMG-Y. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:2505228,ECO:0000303\|PubMed:2701943;Dbxref=PMID:15489334,PMID:2505228,PMID:2701943
P17096	45	73	35	45	Alternative sequence	ID=VSP_002182;Note=In isoform HMG-Y. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:2505228,ECO:0000303\|PubMed:2701943;Dbxref=PMID:15489334,PMID:2505228,PMID:2701943
P17096	45	73	66	107	Alternative sequence	ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10428
P17096	45	73	66	107	Alternative sequence	ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10428
P17096	45	73	53	55	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2EZE
P17096	45	73	53	55	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2EZE
P17096	45	73	2	107	Chain	ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y
P17096	45	73	2	107	Chain	ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y
P17096	45	73	53	63	DNA binding	Note=A.T hook 2
P17096	45	73	53	63	DNA binding	Note=A.T hook 2
P17096	45	73	49	49	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:24275569
P17096	45	73	49	49	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:24275569
P17096	45	73	53	53	Modified residue	Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17924679,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMe
P17096	45	73	53	53	Modified residue	Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17924679,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMe
P17096	45	73	58	58	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Modified residue	Note=Omega-N-methylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Modified residue	Note=Omega-N-methylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Modified residue	Note=Omega-N-methylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Modified residue	Note=Omega-N-methylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Mutagenesis	Note=Decreases methylation by PRMT6. Abolishes methylation by PRMT6%3B when associated with A-60. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Mutagenesis	Note=Decreases methylation by PRMT6. Abolishes methylation by PRMT6%3B when associated with A-60. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Mutagenesis	Note=Decreases methylation by PRMT6. Abolishes methylation by PRMT6%3B when associated with A-58. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Mutagenesis	Note=Decreases methylation by PRMT6. Abolishes methylation by PRMT6%3B when associated with A-58. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	53	77	Region	Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250
P17096	45	73	53	77	Region	Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250
P17096	73	90	66	107	Alternative sequence	ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10428
P17096	73	90	66	107	Alternative sequence	ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10428
P17096	73	90	2	107	Chain	ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y
P17096	73	90	2	107	Chain	ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y
P17096	73	90	78	89	DNA binding	Note=A.T hook 3
P17096	73	90	78	89	DNA binding	Note=A.T hook 3
P17096	73	90	78	78	Modified residue	Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12653562;Dbxref=PMID:12653562
P17096	73	90	78	78	Modified residue	Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12653562;Dbxref=PMID:12653562
P17096	73	90	53	77	Region	Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250
P17096	73	90	53	77	Region	Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250

Lost protein functional features of individual exon skipping events in GTEx.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P17096	45	73	35	45	Alternative sequence	ID=VSP_002182;Note=In isoform HMG-Y. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:2505228,ECO:0000303\|PubMed:2701943;Dbxref=PMID:15489334,PMID:2505228,PMID:2701943
P17096	45	73	35	45	Alternative sequence	ID=VSP_002182;Note=In isoform HMG-Y. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:2505228,ECO:0000303\|PubMed:2701943;Dbxref=PMID:15489334,PMID:2505228,PMID:2701943
P17096	45	73	66	107	Alternative sequence	ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10428
P17096	45	73	66	107	Alternative sequence	ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10428
P17096	45	73	53	55	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2EZE
P17096	45	73	53	55	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2EZE
P17096	45	73	2	107	Chain	ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y
P17096	45	73	2	107	Chain	ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y
P17096	45	73	53	63	DNA binding	Note=A.T hook 2
P17096	45	73	53	63	DNA binding	Note=A.T hook 2
P17096	45	73	49	49	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:24275569
P17096	45	73	49	49	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:24275569;Dbxref=PMID:18669648,PMID:24275569
P17096	45	73	53	53	Modified residue	Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17924679,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMe
P17096	45	73	53	53	Modified residue	Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17924679,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMe
P17096	45	73	58	58	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Modified residue	Note=Omega-N-methylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Modified residue	Note=Omega-N-methylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Modified residue	Note=Asymmetric dimethylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Modified residue	Note=Omega-N-methylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Modified residue	Note=Omega-N-methylarginine%3B by PRMT6%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Mutagenesis	Note=Decreases methylation by PRMT6. Abolishes methylation by PRMT6%3B when associated with A-60. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	58	58	Mutagenesis	Note=Decreases methylation by PRMT6. Abolishes methylation by PRMT6%3B when associated with A-60. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Mutagenesis	Note=Decreases methylation by PRMT6. Abolishes methylation by PRMT6%3B when associated with A-58. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	60	60	Mutagenesis	Note=Decreases methylation by PRMT6. Abolishes methylation by PRMT6%3B when associated with A-58. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16159886;Dbxref=PMID:16159886
P17096	45	73	53	77	Region	Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250
P17096	45	73	53	77	Region	Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250
P17096	73	90	66	107	Alternative sequence	ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10428
P17096	73	90	66	107	Alternative sequence	ID=VSP_018084;Note=In isoform HMG-R. NKGAAKTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ->KNWRRRKRRASRRSPRRRSSDPCVPPAPHWRSSFLLGLDSFAPLPPPPPLPQAHHHHRLWPPPPSSTCALTTTLHSTPAAAGLPWAEWGAVFPWPQFPAPPAHPRIHTCPPGQG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10428
P17096	73	90	2	107	Chain	ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y
P17096	73	90	2	107	Chain	ID=PRO_0000206708;Note=High mobility group protein HMG-I/HMG-Y
P17096	73	90	78	89	DNA binding	Note=A.T hook 3
P17096	73	90	78	89	DNA binding	Note=A.T hook 3
P17096	73	90	78	78	Modified residue	Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12653562;Dbxref=PMID:12653562
P17096	73	90	78	78	Modified residue	Note=Phosphothreonine%3B by HIPK2 and CDC2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12653562;Dbxref=PMID:12653562
P17096	73	90	53	77	Region	Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250
P17096	73	90	53	77	Region	Note=Interaction with HIPK2;Ontology_term=ECO:0000250;evidence=ECO:0000250

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SNVs in the skipped exons for HMGA1

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-DD-A1EG-01	exon_skip_450687	34208514	34208659	34208593	34208593	Frame_Shift_Del	G	-	p.L12fs
LIHC	TCGA-DD-A1EG-01	exon_skip_450689	34208514	34208692	34208593	34208593	Frame_Shift_Del	G	-	p.L12fs
BLCA	TCGA-K4-A6FZ-01	exon_skip_450705 exon_skip_450704	34210489	34210572	34210526	34210526	Frame_Shift_Del	G	-	p.R58fs
LIHC	TCGA-DD-A39Y-01	exon_skip_450707	34211245	34211295	34211287	34211287	Frame_Shift_Del	A	-	p.K89fs
HNSC	TCGA-CN-4723-01	exon_skip_450687	34208514	34208659	34208574	34208574	Nonsense_Mutation	C	A	p.S6*
HNSC	TCGA-CN-4723-01	exon_skip_450689	34208514	34208692	34208574	34208574	Nonsense_Mutation	C	A	p.S6*

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
AM38_CENTRAL_NERVOUS_SYSTEM	34208514	34208692	34208627	34208627	Frame_Shift_Del	C	-	p.R24fs
AM38_CENTRAL_NERVOUS_SYSTEM	34208514	34208659	34208627	34208627	Frame_Shift_Del	C	-	p.R24fs
KMRC2_KIDNEY	34208514	34208692	34208666	34208666	Frame_Shift_Del	C	-	p.P37fs
RXF393_KIDNEY	34208514	34208692	34208568	34208568	Missense_Mutation	C	T	p.S4L
RXF393_KIDNEY	34208514	34208659	34208568	34208568	Missense_Mutation	C	T	p.S4L
HEC108_ENDOMETRIUM	34210489	34210572	34210559	34210559	Missense_Mutation	C	A	p.A69D
LNCAPCLONEFGC_PROSTATE	34210489	34210572	34210562	34210562	Missense_Mutation	C	A	p.A70D

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HMGA1

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HMGA1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HMGA1

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RelatedDrugs for HMGA1

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for HMGA1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
HMGA1	C0011860	Diabetes Mellitus, Non-Insulin-Dependent	1	CTD_human
HMGA1	C0020456	Hyperglycemia	1	CTD_human
HMGA1	C0021655	Insulin Resistance	1	CTD_human
HMGA1	C0023269	leiomyosarcoma	1	CTD_human
HMGA1	C0036341	Schizophrenia	1	PSYGENET
HMGA1	C0042138	Uterine Neoplasms	1	CTD_human
HMGA1	C0524620	Metabolic Syndrome X	1	CTD_human

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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