ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for COL13A1

Gene summary

Gene information	Gene symbol	COL13A1
	Gene ID	1305
	Gene name	collagen type XIII alpha 1 chain
	Synonyms	CMS19\|COLXIIIA1
	Cytomap	10q22.1
	Type of gene	protein-coding
	Description	collagen alpha-1(XIII) chaincollagen, type XIII, alpha 1
	Modification date	20180523
	UniProtAcc	Q5TAT6
	Context	PubMed: COL13A1 [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

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Exon skipping events across known transcript of Ensembl for COL13A1 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 COL13A1

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 COL13A1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_42113	10	71627553:71627561:71631939:71631966:71647211:71647247	71631939:71631966	ENSG00000197467.9	ENST00000520133.1
exon_skip_42114	10	71631939:71631966:71634883:71634919:71637794:71637821	71634883:71634919	ENSG00000197467.9	ENST00000479733.1
exon_skip_42116	10	71631939:71631966:71634883:71634919:71640258:71640309	71634883:71634919	ENSG00000197467.9	ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398968.3,ENST00000398973.3,ENST00000398972.3
exon_skip_42122	10	71631939:71631966:71640258:71640309:71647211:71647247	71640258:71640309	ENSG00000197467.9	ENST00000398974.3
exon_skip_42125	10	71634883:71634919:71637794:71637821:71640258:71640309	71637794:71637821	ENSG00000197467.9	ENST00000479733.1
exon_skip_42128	10	71634883:71634919:71640258:71640309:71647211:71647247	71640258:71640309	ENSG00000197467.9	ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398968.3,ENST00000398973.3,ENST00000398972.3
exon_skip_42130	10	71637794:71637821:71640258:71640309:71647211:71647247	71640258:71640309	ENSG00000197467.9	ENST00000479733.1
exon_skip_42131	10	71648059:71648086:71649169:71649196:71654307:71654334	71649169:71649196	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENS
exon_skip_42132	10	71649169:71649196:71654307:71654334:71654430:71654457	71654307:71654334	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENS
exon_skip_42133	10	71655305:71655332:71657230:71657287:71658452:71658518	71657230:71657287	ENSG00000197467.9	ENST00000398978.3,ENST00000398971.3,ENST00000479733.1,ENST00000356340.3,ENST00000398974.3,ENST00000398964.3,ENST00000398973.3,ENST00000398972.3
exon_skip_42134	10	71655305:71655332:71657230:71657287:71662503:71662611	71657230:71657287	ENSG00000197467.9	ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000357811.3,ENST00000520133.1
exon_skip_42136	10	71655305:71655332:71658452:71658518:71662503:71662611	71658452:71658518	ENSG00000197467.9	ENST00000398969.3,ENST00000520267.1,ENST00000522165.1,ENST00000398968.3
exon_skip_42137	10	71657230:71657287:71658452:71658518:71662503:71662611	71658452:71658518	ENSG00000197467.9	ENST00000398978.3,ENST00000398971.3,ENST00000479733.1,ENST00000356340.3,ENST00000398974.3,ENST00000398964.3,ENST00000398973.3,ENST00000398972.3
exon_skip_42138	10	71665542:71665578:71677044:71677089:71678040:71678073	71677044:71677089	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENS
exon_skip_42139	10	71677044:71677089:71678040:71678073:71678817:71678844	71678040:71678073	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENS
exon_skip_42142	10	71678817:71678844:71681637:71681691:71682463:71682550	71681637:71681691	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENS
exon_skip_42143	10	71682463:71682550:71683557:71683611:71684718:71684763	71683557:71683611	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENS
exon_skip_42144	10	71684718:71684763:71685559:71685628:71686842:71686866	71685559:71685628	ENSG00000197467.9	ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENST00000520133.1
exon_skip_42145	10	71689798:71689843:71690155:71690308:71692315:71692360	71690155:71690308	ENSG00000197467.9	ENST00000398978.3,ENST00000398966.3,ENST00000354547.3,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENST00000398973.3,ENST00000398972.3
exon_skip_42146	10	71689798:71689843:71690155:71690308:71695105:71695147	71690155:71690308	ENSG00000197467.9	ENST00000398969.3,ENST00000517713.1,ENST00000398971.3,ENST00000520267.1,ENST00000398975.2,ENST00000520133.1
exon_skip_42152	10	71690208:71690308:71692315:71692360:71695105:71695147	71692315:71692360	ENSG00000197467.9	ENST00000398978.3,ENST00000398966.3,ENST00000354547.3,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3
exon_skip_42153	10	71690208:71690308:71692315:71692360:71696511:71696538	71692315:71692360	ENSG00000197467.9	ENST00000398973.3,ENST00000398972.3
exon_skip_42154	10	71690208:71690308:71695105:71695147:71696511:71696538	71695105:71695147	ENSG00000197467.9	ENST00000398969.3,ENST00000517713.1,ENST00000398971.3,ENST00000520267.1,ENST00000456019.1,ENST00000398975.2,ENST00000520133.1
exon_skip_42157	10	71692315:71692360:71695105:71695147:71696511:71696538	71695105:71695147	ENSG00000197467.9	ENST00000398978.3,ENST00000398966.3,ENST00000354547.3,ENST00000479733.1,ENST00000522165.1,ENST00000357811.3,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3
exon_skip_42160	10	71697390:71697471:71700743:71700779:71703880:71703934	71700743:71700779	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000354547.3,ENST00000398971.3,ENST00000520267.1,ENST00000398975.2,ENST00000356340.3,ENST00000398974.3,ENST00000398968.3,ENST00000398964.3,ENST00000398972.3
exon_skip_42161	10	71697390:71697471:71703880:71703934:71705426:71705480	71703880:71703934	ENSG00000197467.9	ENST00000517713.1,ENST00000479733.1,ENST00000522165.1,ENST00000357811.3,ENST00000456019.1,ENST00000398973.3,ENST00000520133.1
exon_skip_42162	10	71703880:71703934:71705426:71705480:71707062:71707098	71705426:71705480	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000518052.1,ENST00000357811.3,ENST00000456019.1,ENST00000398975.2,ENST00000356340.3,ENS
exon_skip_42164	10	71707062:71707098:71712637:71712724:71716759:71716798	71712637:71712724	ENSG00000197467.9	ENST00000398969.3,ENST00000398978.3,ENST00000398966.3,ENST00000517713.1,ENST00000354547.3,ENST00000398971.3,ENST00000479733.1,ENST00000520267.1,ENST00000522165.1,ENST00000357811.3,ENST00000456019.1,ENST00000398975.2,ENST00000356340.3,ENST00000398974.3,ENS
exon_skip_42165	10	71707062:71707098:71713703:71713781:71716759:71716798	71713703:71713781	ENSG00000197467.9	ENST00000518052.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for COL13A1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_42113	10	71627553:71627561:71631939:71631966:71647211:71647247	71631939:71631966	ENSG00000197467.9	ENST00000520133.1
exon_skip_42114	10	71631939:71631966:71634883:71634919:71637794:71637821	71634883:71634919	ENSG00000197467.9	ENST00000479733.1
exon_skip_42116	10	71631939:71631966:71634883:71634919:71640258:71640309	71634883:71634919	ENSG00000197467.9	ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000517713.1,ENST00000522165.1
exon_skip_42122	10	71631939:71631966:71640258:71640309:71647211:71647247	71640258:71640309	ENSG00000197467.9	ENST00000398974.3
exon_skip_42125	10	71634883:71634919:71637794:71637821:71640258:71640309	71637794:71637821	ENSG00000197467.9	ENST00000479733.1
exon_skip_42128	10	71634883:71634919:71640258:71640309:71647211:71647247	71640258:71640309	ENSG00000197467.9	ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000517713.1,ENST00000522165.1
exon_skip_42130	10	71637794:71637821:71640258:71640309:71647211:71647247	71640258:71640309	ENSG00000197467.9	ENST00000479733.1
exon_skip_42131	10	71648059:71648086:71649169:71649196:71654307:71654334	71649169:71649196	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENS
exon_skip_42132	10	71649169:71649196:71654307:71654334:71654430:71654457	71654307:71654334	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENS
exon_skip_42133	10	71655305:71655332:71657230:71657287:71658452:71658518	71657230:71657287	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398964.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3
exon_skip_42134	10	71655305:71655332:71657230:71657287:71662503:71662611	71657230:71657287	ENSG00000197467.9	ENST00000398966.3,ENST00000354547.3,ENST00000357811.3,ENST00000517713.1,ENST00000520133.1
exon_skip_42136	10	71655305:71655332:71658452:71658518:71662503:71662611	71658452:71658518	ENSG00000197467.9	ENST00000398968.3,ENST00000398969.3,ENST00000520267.1,ENST00000522165.1
exon_skip_42137	10	71657230:71657287:71658452:71658518:71662503:71662611	71658452:71658518	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398964.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3
exon_skip_42138	10	71665542:71665578:71677044:71677089:71678040:71678073	71677044:71677089	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENS
exon_skip_42139	10	71677044:71677089:71678040:71678073:71678817:71678844	71678040:71678073	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENS
exon_skip_42142	10	71678817:71678844:71681637:71681691:71682463:71682550	71681637:71681691	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENS
exon_skip_42143	10	71682463:71682550:71683557:71683611:71684718:71684763	71683557:71683611	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENS
exon_skip_42144	10	71684718:71684763:71685559:71685628:71686842:71686866	71685559:71685628	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000356340.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENST00000517713.1,ENST00000522165.1,ENST00000520133.1
exon_skip_42145	10	71689798:71689843:71690155:71690308:71692315:71692360	71690155:71690308	ENSG00000197467.9	ENST00000398974.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000522165.1
exon_skip_42146	10	71689798:71689843:71690155:71690308:71695105:71695147	71690155:71690308	ENSG00000197467.9	ENST00000398971.3,ENST00000398969.3,ENST00000520267.1,ENST00000517713.1,ENST00000520133.1,ENST00000398975.2
exon_skip_42151	10	71690155:71690308:71690915:71691012:71692315:71692360	71690915:71691012	ENSG00000197467.9	ENST00000479733.1
exon_skip_42152	10	71690208:71690308:71692315:71692360:71695105:71695147	71692315:71692360	ENSG00000197467.9	ENST00000398974.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000356340.3,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000522165.1
exon_skip_42153	10	71690208:71690308:71692315:71692360:71696511:71696538	71692315:71692360	ENSG00000197467.9	ENST00000398972.3,ENST00000398973.3
exon_skip_42154	10	71690208:71690308:71695105:71695147:71696511:71696538	71695105:71695147	ENSG00000197467.9	ENST00000398971.3,ENST00000398969.3,ENST00000520267.1,ENST00000517713.1,ENST00000520133.1,ENST00000398975.2,ENST00000456019.1
exon_skip_42157	10	71692315:71692360:71695105:71695147:71696511:71696538	71695105:71695147	ENSG00000197467.9	ENST00000398974.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000356340.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000522165.1
exon_skip_42160	10	71697390:71697471:71700743:71700779:71703880:71703934	71700743:71700779	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398978.3,ENST00000354547.3,ENST00000520267.1,ENST00000398975.2
exon_skip_42161	10	71697390:71697471:71703880:71703934:71705426:71705480	71703880:71703934	ENSG00000197467.9	ENST00000398973.3,ENST00000479733.1,ENST00000357811.3,ENST00000517713.1,ENST00000522165.1,ENST00000520133.1,ENST00000456019.1
exon_skip_42162	10	71703880:71703934:71705426:71705480:71707062:71707098	71705426:71705480	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENS
exon_skip_42164	10	71707062:71707098:71712637:71712724:71716759:71716798	71712637:71712724	ENSG00000197467.9	ENST00000398974.3,ENST00000398971.3,ENST00000398968.3,ENST00000398966.3,ENST00000398964.3,ENST00000398969.3,ENST00000356340.3,ENST00000398972.3,ENST00000398973.3,ENST00000479733.1,ENST00000398978.3,ENST00000354547.3,ENST00000357811.3,ENST00000520267.1,ENS
exon_skip_42165	10	71707062:71707098:71713703:71713781:71716759:71716798	71713703:71713781	ENSG00000197467.9	ENST00000518052.1

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 COL13A1

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
ENST00000398978	71634883	71634919	In-frame
ENST00000398978	71640258	71640309	In-frame
ENST00000398978	71649169	71649196	In-frame
ENST00000398978	71654307	71654334	In-frame
ENST00000398978	71657230	71657287	In-frame
ENST00000398978	71658452	71658518	In-frame
ENST00000398978	71677044	71677089	In-frame
ENST00000398978	71678040	71678073	In-frame
ENST00000398978	71681637	71681691	In-frame
ENST00000398978	71683557	71683611	In-frame
ENST00000398978	71685559	71685628	In-frame
ENST00000398978	71690155	71690308	In-frame
ENST00000398978	71692315	71692360	In-frame
ENST00000398978	71695105	71695147	In-frame
ENST00000398978	71700743	71700779	In-frame
ENST00000398978	71705426	71705480	In-frame
ENST00000398978	71712637	71712724	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
ENST00000398978	71634883	71634919	In-frame
ENST00000398978	71640258	71640309	In-frame
ENST00000398978	71649169	71649196	In-frame
ENST00000398978	71654307	71654334	In-frame
ENST00000398978	71657230	71657287	In-frame
ENST00000398978	71658452	71658518	In-frame
ENST00000398978	71677044	71677089	In-frame
ENST00000398978	71678040	71678073	In-frame
ENST00000398978	71681637	71681691	In-frame
ENST00000398978	71683557	71683611	In-frame
ENST00000398978	71685559	71685628	In-frame
ENST00000398978	71690155	71690308	In-frame
ENST00000398978	71692315	71692360	In-frame
ENST00000398978	71695105	71695147	In-frame
ENST00000398978	71700743	71700779	In-frame
ENST00000398978	71705426	71705480	In-frame
ENST00000398978	71712637	71712724	In-frame

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Infer the effects of exon skipping event on protein functional features for COL13A1

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
ENST00000398978	3110	717	71634883	71634919	892	927	133	145
ENST00000398978	3110	717	71640258	71640309	928	978	145	162
ENST00000398978	3110	717	71657230	71657287	1150	1206	219	238
ENST00000398978	3110	717	71658452	71658518	1207	1272	238	260
ENST00000398978	3110	717	71677044	71677089	1444	1488	317	332
ENST00000398978	3110	717	71678040	71678073	1489	1521	332	343
ENST00000398978	3110	717	71681637	71681691	1549	1602	352	370
ENST00000398978	3110	717	71683557	71683611	1690	1743	399	417
ENST00000398978	3110	717	71685559	71685628	1789	1857	432	455
ENST00000398978	3110	717	71690155	71690308	1990	2142	499	550
ENST00000398978	3110	717	71692315	71692360	2143	2187	550	565
ENST00000398978	3110	717	71695105	71695147	2188	2229	565	579
ENST00000398978	3110	717	71700743	71700779	2338	2373	615	627
ENST00000398978	3110	717	71705426	71705480	2428	2481	645	663
ENST00000398978	3110	717	71712637	71712724	2518	2604	675	704

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
ENST00000398978	3110	717	71634883	71634919	892	927	133	145
ENST00000398978	3110	717	71640258	71640309	928	978	145	162
ENST00000398978	3110	717	71657230	71657287	1150	1206	219	238
ENST00000398978	3110	717	71658452	71658518	1207	1272	238	260
ENST00000398978	3110	717	71677044	71677089	1444	1488	317	332
ENST00000398978	3110	717	71678040	71678073	1489	1521	332	343
ENST00000398978	3110	717	71681637	71681691	1549	1602	352	370
ENST00000398978	3110	717	71683557	71683611	1690	1743	399	417
ENST00000398978	3110	717	71685559	71685628	1789	1857	432	455
ENST00000398978	3110	717	71690155	71690308	1990	2142	499	550
ENST00000398978	3110	717	71692315	71692360	2143	2187	550	565
ENST00000398978	3110	717	71695105	71695147	2188	2229	565	579
ENST00000398978	3110	717	71700743	71700779	2338	2373	615	627
ENST00000398978	3110	717	71705426	71705480	2428	2481	645	663
ENST00000398978	3110	717	71712637	71712724	2518	2604	675	704

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

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

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SNVs in the skipped exons for COL13A1

- 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.

COL13A1_LUAD_exon_skip_42139_psi_boxplot.png
boxplot

- 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_42114 exon_skip_42116	71634884	71634919	71634890	71634890	Frame_Shift_Del	A	-	p.K136fs
COAD	TCGA-AD-5900-01	exon_skip_42130 exon_skip_42122 exon_skip_42128	71640259	71640309	71640303	71640303	Frame_Shift_Del	C	-	p.G160fs
LIHC	TCGA-DD-A39Y-01	exon_skip_42130 exon_skip_42122 exon_skip_42128	71640259	71640309	71640303	71640303	Frame_Shift_Del	C	-	p.G160fs
ESCA	TCGA-L5-A4OI-01	exon_skip_42136 exon_skip_42137	71658453	71658518	71658500	71658500	Frame_Shift_Del	A	-	p.I254fs
ESCA	TCGA-L5-A4OI-01	exon_skip_42136 exon_skip_42137	71658453	71658518	71658500	71658500	Frame_Shift_Del	A	-	p.R256fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_42142	71681638	71681691	71681646	71681646	Frame_Shift_Del	G	-	p.K355fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_42142	71681638	71681691	71681682	71681682	Frame_Shift_Del	G	-	p.L367fs
UCEC	TCGA-AX-A05Y-01	exon_skip_42143	71683558	71683611	71683587	71683587	Frame_Shift_Del	C	-	p.G409fs
LIHC	TCGA-DD-A3A0-01	exon_skip_42143	71683558	71683611	71683594	71683594	Frame_Shift_Del	G	-	p.G412fs
STAD	TCGA-D7-A6EY-01	exon_skip_42145 exon_skip_42146	71690156	71690308	71690203	71690203	Frame_Shift_Del	C	-	p.G515fs
STAD	TCGA-CD-A4MJ-01	exon_skip_42145 exon_skip_42146	71690156	71690308	71690277	71690277	Frame_Shift_Del	A	-	p.E540fs
LIHC	TCGA-DD-A3A0-01	exon_skip_42161	71703881	71703934	71703922	71703922	Frame_Shift_Del	A	-	p.P641fs
LIHC	TCGA-DD-A3A0-01	exon_skip_42164	71712638	71712724	71712711	71712711	Frame_Shift_Del	C	-	p.A700fs
LIHC	TCGA-DD-A39Y-01	exon_skip_42164	71712638	71712724	71712718	71712718	Frame_Shift_Del	C	-	p.C702fs
UCEC	TCGA-AP-A0LM-01	exon_skip_42144	71685560	71685628	71685584	71685584	Nonsense_Mutation	G	T	p.G441*
KIRC	TCGA-CJ-4634-01	exon_skip_42152 exon_skip_42153	71692316	71692360	71692319	71692319	Nonsense_Mutation	G	T	p.E552X
THYM	TCGA-X7-A8D8-01	exon_skip_42130 exon_skip_42122 exon_skip_42128	71640259	71640309	71640310	71640310	Splice_Site	G	T	.
UCEC	TCGA-BG-A0VZ-01	exon_skip_42132	71654308	71654334	71654307	71654307	Splice_Site	G	T	e10-1
UCEC	TCGA-BG-A0VZ-01	exon_skip_42132	71654308	71654334	71654307	71654307	Splice_Site	G	T	p.G193_splice
SKCM	TCGA-EE-A3AE-06	exon_skip_42134 exon_skip_42133	71657231	71657287	71657230	71657230	Splice_Site	G	A	.
LUAD	TCGA-86-6851-01	exon_skip_42139	71678041	71678073	71678040	71678040	Splice_Site	G	T	p.G333_splice

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-86-6851-01
	Cancer type: LUAD
	ESID: exon_skip_42139
	Skipped exon start: 71678041
	Skipped exon end: 71678073
	Mutation start: 71678040
	Mutation end: 71678040
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: T
	AAchange: p.G333_splice
exon_skip_115375_LUAD_TCGA-86-6851-01.png
exon_skip_42139_LUAD_TCGA-86-6851-01.png
exon_skip_489149_LUAD_TCGA-86-6851-01.png
	Sample: TCGA-BG-A0VZ-01
	Cancer type: UCEC
	ESID: exon_skip_42132
	Skipped exon start: 71654308
	Skipped exon end: 71654334
	Mutation start: 71654307
	Mutation end: 71654307
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: T
	AAchange: p.G193_splice
	Sample: TCGA-BG-A0VZ-01
	Cancer type: UCEC
	ESID: exon_skip_42132
	Skipped exon start: 71654308
	Skipped exon end: 71654334
	Mutation start: 71654307
	Mutation end: 71654307
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: T
	AAchange: e10-1
exon_skip_42132_UCEC_TCGA-BG-A0VZ-01.png

- 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
HEC59_ENDOMETRIUM	71658453	71658518	71658500	71658500	Frame_Shift_Del	A	-	p.I254fs
HEC108_ENDOMETRIUM	71690156	71690308	71690203	71690203	Frame_Shift_Del	C	-	p.G515fs
IM95_STOMACH	71690156	71690308	71690203	71690203	Frame_Shift_Del	C	-	p.G515fs
DU145_PROSTATE	71640259	71640309	71640302	71640303	Frame_Shift_Ins	-	C	p.GP160fs
HCC202_BREAST	71634884	71634919	71634896	71634896	Missense_Mutation	G	A	p.A138T
CASKI_CERVIX	71634884	71634919	71634912	71634912	Missense_Mutation	G	C	p.G143A
HS739T_FIBROBLAST	71634884	71634919	71634914	71634914	Missense_Mutation	C	T	p.R144C
NCIBL2009_MATCHED_NORMAL_TISSUE	71640259	71640309	71640266	71640266	Missense_Mutation	C	A	p.P148H
JHUEM2_ENDOMETRIUM	71640259	71640309	71640271	71640271	Missense_Mutation	G	A	p.D150N
SNUC5_LARGE_INTESTINE	71640259	71640309	71640301	71640301	Missense_Mutation	G	A	p.G160S
NCIH1155_LUNG	71658453	71658518	71658474	71658474	Missense_Mutation	G	C	p.V246L
NCIH727_LUNG	71658453	71658518	71658492	71658492	Missense_Mutation	C	A	p.P252T
DOV13_OVARY	71658453	71658518	71658511	71658512	Missense_Mutation	CG	TA	p.T258I
HS294T_SKIN	71658453	71658518	71658511	71658511	Missense_Mutation	C	T	p.T258M
MYLA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	71678041	71678073	71678050	71678050	Missense_Mutation	G	A	p.G336R
OVTOKO_OVARY	71681638	71681691	71681648	71681648	Missense_Mutation	G	A	p.G356E
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	71681638	71681691	71681659	71681659	Missense_Mutation	T	C	p.S360P
NCIH1568_LUNG	71681638	71681691	71681683	71681683	Missense_Mutation	G	T	p.G368W
MCC13_SKIN	71690156	71690308	71690183	71690183	Missense_Mutation	G	A	p.G509S
MM415_SKIN	71690156	71690308	71690195	71690195	Missense_Mutation	C	T	p.P513S
NCIH64_LUNG	71690156	71690308	71690228	71690229	Missense_Mutation	GG	TT	p.G524L
NCIH650_LUNG	71690156	71690308	71690245	71690245	Missense_Mutation	C	G	p.N529K
SNU1040_LARGE_INTESTINE	71695106	71695147	71695118	71695118	Missense_Mutation	C	T	p.P570S
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	71700744	71700779	71700748	71700748	Missense_Mutation	C	A	p.A617D
HCC2157_BREAST	71703881	71703934	71703929	71703929	Missense_Mutation	G	A	p.E644K
HCC2157_MATCHED_NORMAL_TISSUE	71703881	71703934	71703929	71703929	Missense_Mutation	G	A	p.E644K
NCIH2342_LUNG	71712638	71712724	71712655	71712655	Missense_Mutation	A	C	p.K681N
FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	71712638	71712724	71712698	71712698	Missense_Mutation	C	T	p.P696S
UMC11_LUNG	71654308	71654334	71654329	71654329	Nonsense_Mutation	C	T	p.Q200*
SW756_CERVIX	71681638	71681691	71681641	71681641	Nonsense_Mutation	G	T	p.E354*
CCLFPEDS0008T_SOFT_TISSUE	71703881	71703934	71703890	71703890	Nonsense_Mutation	G	T	p.G631*
NCIH1568_LUNG	71649170	71649196	71649196	71649196	Splice_Site	G	C	p.M192I
MZ7MEL_SKIN	71683558	71683611	71683558	71683558	Splice_Site	G	A	p.G400R

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COL13A1

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 COL13A1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COL13A1

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RelatedDrugs for COL13A1

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 COL13A1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
COL13A1	C0000786	Spontaneous abortion	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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