|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for COL9A1 |
 Gene summary |
| Gene information | Gene symbol | COL9A1 | Gene ID | 1297 |
| Gene name | collagen type IX alpha 1 chain | |
| Synonyms | DJ149L1.1.2|EDM6|MED|STL4 | |
| Cytomap | 6q13 | |
| Type of gene | protein-coding | |
| Description | collagen alpha-1(IX) chainalpha-1(IX) collagen chaincartilage-specific short collagencollagen IX, alpha-1 polypeptidecollagen, type IX, alpha 1 | |
| Modification date | 20180523 | |
| UniProtAcc | P20849 | |
| Context | PubMed: COL9A1 [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 |
Top |
Exon skipping events across known transcript of Ensembl for COL9A1 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. |
 |
Top |
Gene isoform structures and expression levels for COL9A1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for COL9A1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_460429 | 6 | 70944262:70944296:70944496:70944643:70948956:70948989 | 70944496:70944643 | ENSG00000112280.11 | ENST00000447041.2,ENST00000370499.4,ENST00000489611.1,ENST00000357250.6,ENST00000486080.1,ENST00000320755.7 |
| exon_skip_460430 | 6 | 70951121:70951157:70951666:70951738:70952364:70952418 | 70951666:70951738 | ENSG00000112280.11 | ENST00000447041.2,ENST00000370499.4,ENST00000360859.6,ENST00000357250.6,ENST00000493682.2,ENST00000320755.7 |
| exon_skip_460431 | 6 | 70961964:70962018:70962960:70963003:70963087:70963132 | 70962960:70963003 | ENSG00000112280.11 | ENST00000447041.2 |
| exon_skip_460432 | 6 | 70961964:70962018:70963087:70963132:70964178:70964232 | 70963087:70963132 | ENSG00000112280.11 | ENST00000370499.4,ENST00000360859.6,ENST00000489611.1,ENST00000357250.6,ENST00000493682.2,ENST00000320755.7,ENST00000489861.2 |
| exon_skip_460435 | 6 | 70979335:70979368:70980016:70980070:70981357:70981411 | 70980016:70980070 | ENSG00000112280.11 | ENST00000370499.4,ENST00000357250.6,ENST00000320755.7 |
| exon_skip_460437 | 6 | 70984421:70984475:70990514:70990577:70990706:70990742 | 70990514:70990577 | ENSG00000112280.11 | ENST00000370499.4,ENST00000357250.6,ENST00000320755.7 |
| exon_skip_460440 | 6 | 70993439:70993523:71003869:71004266:71009745:71009878 | 71003869:71004266 | ENSG00000112280.11 | ENST00000357250.6,ENST00000370496.3 |
| exon_skip_460442 | 6 | 71003869:71004266:71009745:71009878:71010011:71010089 | 71009745:71009878 | ENSG00000112280.11 | ENST00000357250.6,ENST00000370496.3 |
| exon_skip_460443 | 6 | 71010011:71010089:71011703:71011777:71012613:71012773 | 71011703:71011777 | ENSG00000112280.11 | ENST00000370496.3 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for COL9A1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_460429 | 6 | 70944262:70944296:70944496:70944643:70948956:70948989 | 70944496:70944643 | ENSG00000112280.11 | ENST00000357250.6,ENST00000320755.7,ENST00000370499.4,ENST00000486080.1,ENST00000489611.1,ENST00000447041.2 |
| exon_skip_460430 | 6 | 70951121:70951157:70951666:70951738:70952364:70952418 | 70951666:70951738 | ENSG00000112280.11 | ENST00000357250.6,ENST00000320755.7,ENST00000370499.4,ENST00000447041.2,ENST00000493682.2,ENST00000360859.6 |
| exon_skip_460431 | 6 | 70961964:70962018:70962960:70963003:70963087:70963132 | 70962960:70963003 | ENSG00000112280.11 | ENST00000447041.2 |
| exon_skip_460432 | 6 | 70961964:70962018:70963087:70963132:70964178:70964232 | 70963087:70963132 | ENSG00000112280.11 | ENST00000357250.6,ENST00000320755.7,ENST00000370499.4,ENST00000489611.1,ENST00000493682.2,ENST00000360859.6,ENST00000489861.2 |
| exon_skip_460435 | 6 | 70979335:70979368:70980016:70980070:70981357:70981411 | 70980016:70980070 | ENSG00000112280.11 | ENST00000357250.6,ENST00000320755.7,ENST00000370499.4 |
| exon_skip_460437 | 6 | 70984421:70984475:70990514:70990577:70990706:70990742 | 70990514:70990577 | ENSG00000112280.11 | ENST00000357250.6,ENST00000320755.7,ENST00000370499.4 |
| exon_skip_460440 | 6 | 70993439:70993523:71003869:71004266:71009745:71009878 | 71003869:71004266 | ENSG00000112280.11 | ENST00000357250.6,ENST00000370496.3 |
| exon_skip_460442 | 6 | 71003869:71004266:71009745:71009878:71010011:71010089 | 71009745:71009878 | ENSG00000112280.11 | ENST00000357250.6,ENST00000370496.3 |
| exon_skip_460443 | 6 | 71010011:71010089:71011703:71011777:71012613:71012773 | 71011703:71011777 | ENSG00000112280.11 | ENST00000370496.3 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for COL9A1 |
| 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 |
| ENST00000357250 | 71003869 | 71004266 | Frame-shift |
| ENST00000357250 | 71009745 | 71009878 | Frame-shift |
| ENST00000357250 | 70944496 | 70944643 | In-frame |
| ENST00000357250 | 70951666 | 70951738 | In-frame |
| ENST00000357250 | 70963087 | 70963132 | In-frame |
| ENST00000357250 | 70980016 | 70980070 | In-frame |
| ENST00000357250 | 70990514 | 70990577 | 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 |
| ENST00000357250 | 71003869 | 71004266 | Frame-shift |
| ENST00000357250 | 71009745 | 71009878 | Frame-shift |
| ENST00000357250 | 70944496 | 70944643 | In-frame |
| ENST00000357250 | 70951666 | 70951738 | In-frame |
| ENST00000357250 | 70963087 | 70963132 | In-frame |
| ENST00000357250 | 70980016 | 70980070 | In-frame |
| ENST00000357250 | 70990514 | 70990577 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for COL9A1 |
| 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 |
| ENST00000357250 | 4778 | 921 | 70990514 | 70990577 | 1072 | 1134 | 304 | 325 |
| ENST00000357250 | 4778 | 921 | 70980016 | 70980070 | 1303 | 1356 | 381 | 399 |
| ENST00000357250 | 4778 | 921 | 70963087 | 70963132 | 1879 | 1923 | 573 | 588 |
| ENST00000357250 | 4778 | 921 | 70951666 | 70951738 | 2086 | 2157 | 642 | 666 |
| ENST00000357250 | 4778 | 921 | 70944496 | 70944643 | 2272 | 2418 | 704 | 753 |
| 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 |
| ENST00000357250 | 4778 | 921 | 70990514 | 70990577 | 1072 | 1134 | 304 | 325 |
| ENST00000357250 | 4778 | 921 | 70980016 | 70980070 | 1303 | 1356 | 381 | 399 |
| ENST00000357250 | 4778 | 921 | 70963087 | 70963132 | 1879 | 1923 | 573 | 588 |
| ENST00000357250 | 4778 | 921 | 70951666 | 70951738 | 2086 | 2157 | 642 | 666 |
| ENST00000357250 | 4778 | 921 | 70944496 | 70944643 | 2272 | 2418 | 704 | 753 |
| 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 |
Top |
SNVs in the skipped exons for COL9A1 |
| - 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-A3A0-01 | exon_skip_460437 | 70990515 | 70990577 | 70990555 | 70990555 | Frame_Shift_Del | T | - | p.K312fs |
| LIHC | TCGA-ED-A7XP-01 | exon_skip_460440 | 71003870 | 71004266 | 71003965 | 71003965 | Frame_Shift_Del | T | - | p.I201fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_460440 | 71003870 | 71004266 | 71004044 | 71004044 | Frame_Shift_Del | G | - | p.S174fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_460442 | 71009746 | 71009878 | 71009776 | 71009776 | Frame_Shift_Del | C | - | p.G90fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_460440 | 71003870 | 71004266 | 71004260 | 71004261 | Frame_Shift_Ins | - | A | p.L102fs |
| LUAD | TCGA-05-4410-01 | exon_skip_460429 | 70944497 | 70944643 | 70944628 | 70944628 | Nonsense_Mutation | C | A | p.E710* |
| BLCA | TCGA-CF-A47S-01 | exon_skip_460440 | 71003870 | 71004266 | 71004166 | 71004166 | Nonsense_Mutation | G | A | p.Q134* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_460440 | 71003870 | 71004266 | 71004214 | 71004214 | Nonsense_Mutation | G | A | p.R118* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_460440 | 71003870 | 71004266 | 71004214 | 71004214 | Nonsense_Mutation | G | A | p.R118X |
| - 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 |
| EKVX_LUNG | 71003870 | 71004266 | 71004090 | 71004090 | Frame_Shift_Del | C | - | p.G159fs |
| OC316_OVARY | 70944497 | 70944643 | 70944592 | 70944593 | Frame_Shift_Ins | - | C | p.L722fs |
| MEWO_SKIN | 70944497 | 70944643 | 70944541 | 70944541 | Missense_Mutation | C | T | p.G739R |
| DAOY_CENTRAL_NERVOUS_SYSTEM | 70944497 | 70944643 | 70944542 | 70944542 | Missense_Mutation | C | A | p.Q738H |
| SUIT2_PANCREAS | 70944497 | 70944643 | 70944552 | 70944552 | Missense_Mutation | C | T | p.R735Q |
| RKO_LARGE_INTESTINE | 70944497 | 70944643 | 70944562 | 70944562 | Missense_Mutation | G | A | p.P732S |
| IPC298_SKIN | 70944497 | 70944643 | 70944589 | 70944589 | Missense_Mutation | G | A | p.P723S |
| MM415_SKIN | 70944497 | 70944643 | 70944603 | 70944603 | Missense_Mutation | C | T | p.G718E |
| SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70944497 | 70944643 | 70944613 | 70944613 | Missense_Mutation | C | T | p.G715R |
| ISTMEL1_SKIN | 70944497 | 70944643 | 70944615 | 70944615 | Missense_Mutation | C | T | p.R714K |
| COLO684_ENDOMETRIUM | 70951667 | 70951738 | 70951681 | 70951681 | Missense_Mutation | T | C | p.M662V |
| MEWO_SKIN | 70951667 | 70951738 | 70951692 | 70951692 | Missense_Mutation | C | T | p.G658E |
| SNU1214_UPPER_AERODIGESTIVE_TRACT | 70951667 | 70951738 | 70951704 | 70951704 | Missense_Mutation | G | A | p.P654L |
| RERFLCFM_LUNG | 70963088 | 70963132 | 70963095 | 70963095 | Missense_Mutation | C | A | p.G586V |
| PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70963088 | 70963132 | 70963129 | 70963129 | Missense_Mutation | C | T | p.V575I |
| BE13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70963088 | 70963132 | 70963129 | 70963129 | Missense_Mutation | C | T | p.V575I |
| SNU1040_LARGE_INTESTINE | 70980017 | 70980070 | 70980033 | 70980033 | Missense_Mutation | C | T | p.G394D |
| YD38_UPPER_AERODIGESTIVE_TRACT | 70980017 | 70980070 | 70980046 | 70980046 | Missense_Mutation | G | A | p.P390S |
| P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 70990515 | 70990577 | 70990558 | 70990558 | Missense_Mutation | C | T | p.G311E |
| ESS1_ENDOMETRIUM | 71003870 | 71004266 | 71003889 | 71003889 | Missense_Mutation | T | G | p.N226T |
| SISO_CERVIX | 71003870 | 71004266 | 71003922 | 71003922 | Missense_Mutation | T | A | p.D215V |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 71003870 | 71004266 | 71003922 | 71003922 | Missense_Mutation | T | A | p.D215V |
| SNU1079_BILIARY_TRACT | 71003870 | 71004266 | 71003932 | 71003932 | Missense_Mutation | T | C | p.I212V |
| NCIH1568_LUNG | 71003870 | 71004266 | 71003989 | 71003989 | Missense_Mutation | T | C | p.T193A |
| A2780_OVARY | 71003870 | 71004266 | 71004014 | 71004014 | Missense_Mutation | C | A | p.M184I |
| CORL88_LUNG | 71003870 | 71004266 | 71004048 | 71004048 | Missense_Mutation | G | A | p.S173F |
| T84_LARGE_INTESTINE | 71003870 | 71004266 | 71004057 | 71004057 | Missense_Mutation | G | A | p.S170L |
| HUH1_LIVER | 71003870 | 71004266 | 71004079 | 71004079 | Missense_Mutation | T | G | p.S163R |
| SNU175_LARGE_INTESTINE | 71003870 | 71004266 | 71004138 | 71004138 | Missense_Mutation | C | T | p.G143D |
| OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 71003870 | 71004266 | 71004188 | 71004188 | Missense_Mutation | C | A | p.K126N |
| HCC2157_MATCHED_NORMAL_TISSUE | 71003870 | 71004266 | 71004213 | 71004213 | Missense_Mutation | C | T | p.R118Q |
| KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 71009746 | 71009878 | 71009847 | 71009847 | Missense_Mutation | A | C | p.D66E |
| MOGGCCM_CENTRAL_NERVOUS_SYSTEM | 71009746 | 71009878 | 71009851 | 71009851 | Missense_Mutation | A | T | p.V65E |
| NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 71009746 | 71009878 | 71009856 | 71009856 | Missense_Mutation | G | T | p.F63L |
| CAL78_BONE | 71011704 | 71011777 | 71011707 | 71011707 | Missense_Mutation | G | T | p.P29T |
| CP66MEL_SKIN | 71011704 | 71011777 | 71011707 | 71011707 | Missense_Mutation | G | T | p.P29T |
| CAL78_BONE | 71011704 | 71011777 | 71011710 | 71011710 | Missense_Mutation | G | T | p.R28S |
| SNU1040_LARGE_INTESTINE | 71011704 | 71011777 | 71011724 | 71011724 | Missense_Mutation | G | A | p.A23V |
| CALU3_LUNG | 71011704 | 71011777 | 71011749 | 71011749 | Missense_Mutation | T | A | p.S15C |
| SBC5_LUNG | 70980017 | 70980070 | 70980069 | 70980069 | Splice_Site | C | A | p.G382V |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COL9A1 |
| 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 |
| exon_skip_460432 | 6 | 70961964:70962018:70963087:70963132:70964178:70964232 | 70963087:70963132 | ENST00000370499.4,ENST00000360859.6,ENST00000489611.1,ENST00000357250.6,ENST00000493682.2,ENST00000320755.7,ENST00000489861.2 | STAD | rs9346373 | chr6:70963124 | A/C | 7.71e-04 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COL9A1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COL9A1 |
Top |
RelatedDrugs for COL9A1 |
| 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 |
Top |
RelatedDiseases for COL9A1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| COL9A1 | C0029422 | Osteochondrodysplasias | 2 | CTD_human |
| COL9A1 | C0018784 | Sensorineural Hearing Loss (disorder) | 1 | CTD_human;HPO |
| COL9A1 | C0027092 | Myopia | 1 | CTD_human;HPO |
| COL9A1 | C0035309 | Retinal Diseases | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|