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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for ITGA1 |
 Gene summary |
| Gene information | Gene symbol | ITGA1 | Gene ID | 3672 |
| Gene name | integrin subunit alpha 1 | |
| Synonyms | CD49a|VLA1 | |
| Cytomap | 5q11.2 | |
| Type of gene | protein-coding | |
| Description | integrin alpha-1CD49 antigen-like family member AVLA-1laminin and collagen receptorvery late activation protein 1 | |
| Modification date | 20180522 | |
| UniProtAcc | P56199 | |
| Context | PubMed: ITGA1 [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 |
| ITGA1 | GO:0032516 | positive regulation of phosphoprotein phosphatase activity | 15592458 |
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Exon skipping events across known transcript of Ensembl for ITGA1 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 ITGA1 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for ITGA1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_434719 | 5 | 52194068:52194213:52201592:52201738:52204727:52204871 | 52201592:52201738 | ENSG00000213949.4 | ENST00000282588.6 |
| exon_skip_434721 | 5 | 52214561:52214728:52216161:52216298:52218606:52218717 | 52216161:52216298 | ENSG00000213949.4 | ENST00000504669.1,ENST00000282588.6 |
| exon_skip_434723 | 5 | 52225454:52225531:52227876:52227966:52229723:52229826 | 52227876:52227966 | ENSG00000213949.4 | ENST00000504669.1,ENST00000282588.6 |
| exon_skip_434724 | 5 | 52235419:52235521:52235669:52235774:52240772:52240865 | 52235669:52235774 | ENSG00000213949.4 | ENST00000504669.1,ENST00000282588.6,ENST00000506275.1 |
| exon_skip_434725 | 5 | 52235669:52235774:52240772:52240865:52243174:52243291 | 52240772:52240865 | ENSG00000213949.4 | ENST00000504669.1,ENST00000282588.6,ENST00000506275.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for ITGA1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_434719 | 5 | 52194068:52194213:52201592:52201738:52204727:52204871 | 52201592:52201738 | ENSG00000213949.4 | ENST00000282588.6 |
| exon_skip_434721 | 5 | 52214561:52214728:52216161:52216298:52218606:52218717 | 52216161:52216298 | ENSG00000213949.4 | ENST00000282588.6,ENST00000504669.1 |
| exon_skip_434723 | 5 | 52225454:52225531:52227876:52227966:52229723:52229826 | 52227876:52227966 | ENSG00000213949.4 | ENST00000282588.6,ENST00000504669.1 |
| exon_skip_434724 | 5 | 52235419:52235521:52235669:52235774:52240772:52240865 | 52235669:52235774 | ENSG00000213949.4 | ENST00000282588.6,ENST00000504669.1,ENST00000506275.1 |
| exon_skip_434725 | 5 | 52235669:52235774:52240772:52240865:52243174:52243291 | 52240772:52240865 | ENSG00000213949.4 | ENST00000282588.6,ENST00000504669.1,ENST00000506275.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for ITGA1 |
| 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 |
| ENST00000282588 | 52201592 | 52201738 | Frame-shift |
| ENST00000282588 | 52216161 | 52216298 | Frame-shift |
| ENST00000282588 | 52227876 | 52227966 | In-frame |
| ENST00000282588 | 52235669 | 52235774 | In-frame |
| ENST00000282588 | 52240772 | 52240865 | 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 |
| ENST00000282588 | 52201592 | 52201738 | Frame-shift |
| ENST00000282588 | 52216161 | 52216298 | Frame-shift |
| ENST00000282588 | 52227876 | 52227966 | In-frame |
| ENST00000282588 | 52235669 | 52235774 | In-frame |
| ENST00000282588 | 52240772 | 52240865 | In-frame |
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Infer the effects of exon skipping event on protein functional features for ITGA1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
| ENST00000282588 | 10774 | 1179 | 52227876 | 52227966 | 3230 | 3319 | 924 | 953 |
| ENST00000282588 | 10774 | 1179 | 52235669 | 52235774 | 3639 | 3743 | 1060 | 1095 |
| ENST00000282588 | 10774 | 1179 | 52240772 | 52240865 | 3744 | 3836 | 1095 | 1126 |
| 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 |
| ENST00000282588 | 10774 | 1179 | 52227876 | 52227966 | 3230 | 3319 | 924 | 953 |
| ENST00000282588 | 10774 | 1179 | 52235669 | 52235774 | 3639 | 3743 | 1060 | 1095 |
| ENST00000282588 | 10774 | 1179 | 52240772 | 52240865 | 3744 | 3836 | 1095 | 1126 |
| 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 |
| P56199 | 924 | 953 | 29 | 1179 | Chain | ID=PRO_0000174215;Note=Integrin alpha-1 |
| P56199 | 924 | 953 | 939 | 939 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 924 | 953 | 29 | 1141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1060 | 1095 | 29 | 1179 | Chain | ID=PRO_0000174215;Note=Integrin alpha-1 |
| P56199 | 1060 | 1095 | 1030 | 1062 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P56199 | 1060 | 1095 | 1065 | 1072 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P56199 | 1060 | 1095 | 1073 | 1073 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1060 | 1095 | 1083 | 1083 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1060 | 1095 | 29 | 1141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1095 | 1126 | 29 | 1179 | Chain | ID=PRO_0000174215;Note=Integrin alpha-1 |
| P56199 | 1095 | 1126 | 1102 | 1102 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1095 | 1126 | 1113 | 1113 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1095 | 1126 | 1108 | 1108 | Natural variant | ID=VAR_034024;Note=E->G;Dbxref=dbSNP:rs988574 |
| P56199 | 1095 | 1126 | 29 | 1141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| P56199 | 924 | 953 | 29 | 1179 | Chain | ID=PRO_0000174215;Note=Integrin alpha-1 |
| P56199 | 924 | 953 | 939 | 939 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 924 | 953 | 29 | 1141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1060 | 1095 | 29 | 1179 | Chain | ID=PRO_0000174215;Note=Integrin alpha-1 |
| P56199 | 1060 | 1095 | 1030 | 1062 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P56199 | 1060 | 1095 | 1065 | 1072 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P56199 | 1060 | 1095 | 1073 | 1073 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1060 | 1095 | 1083 | 1083 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1060 | 1095 | 29 | 1141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1095 | 1126 | 29 | 1179 | Chain | ID=PRO_0000174215;Note=Integrin alpha-1 |
| P56199 | 1095 | 1126 | 1102 | 1102 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1095 | 1126 | 1113 | 1113 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P56199 | 1095 | 1126 | 1108 | 1108 | Natural variant | ID=VAR_034024;Note=E->G;Dbxref=dbSNP:rs988574 |
| P56199 | 1095 | 1126 | 29 | 1141 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for ITGA1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - 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 |
| ESCA | TCGA-VR-A8Q7-01 | exon_skip_434721 | 52216162 | 52216298 | 52216167 | 52216167 | Nonsense_Mutation | C | T | p.Q721X |
| BLCA | TCGA-DK-A6AW-01 | exon_skip_434721 | 52216162 | 52216298 | 52216260 | 52216260 | Nonsense_Mutation | C | T | p.R752* |
| SKCM | TCGA-DA-A1I1-06 | exon_skip_434721 | 52216162 | 52216298 | 52216260 | 52216260 | Nonsense_Mutation | C | T | p.R752* |
| SKCM | TCGA-DA-A1I1-06 | exon_skip_434721 | 52216162 | 52216298 | 52216260 | 52216260 | Nonsense_Mutation | C | T | p.R752X |
| - 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 |
| SW1353_BONE | 52216162 | 52216298 | 52216210 | 52216211 | Frame_Shift_Ins | - | T | p.SF735fs |
| K029AX_SKIN | 52201593 | 52201738 | 52201682 | 52201682 | Missense_Mutation | A | G | p.I467V |
| OVKATE_OVARY | 52201593 | 52201738 | 52201682 | 52201682 | Missense_Mutation | A | G | p.I467V |
| MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 52216162 | 52216298 | 52216171 | 52216171 | Missense_Mutation | A | G | p.Y722C |
| UMUC16_URINARY_TRACT | 52216162 | 52216298 | 52216185 | 52216185 | Missense_Mutation | G | C | p.D727H |
| NCIH446_LUNG | 52216162 | 52216298 | 52216218 | 52216218 | Missense_Mutation | T | A | p.S738T |
| SNU738_CENTRAL_NERVOUS_SYSTEM | 52216162 | 52216298 | 52216275 | 52216275 | Missense_Mutation | A | G | p.T757A |
| FUOV1_OVARY | 52227877 | 52227966 | 52227884 | 52227884 | Missense_Mutation | G | A | p.E927K |
| KPNYS_AUTONOMIC_GANGLIA | 52227877 | 52227966 | 52227884 | 52227884 | Missense_Mutation | G | A | p.E927K |
| RCM1_LARGE_INTESTINE | 52227877 | 52227966 | 52227884 | 52227884 | Missense_Mutation | G | A | p.E927K |
| CROAP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 52227877 | 52227966 | 52227944 | 52227944 | Missense_Mutation | G | A | p.E947K |
| NCIH2110_LUNG | 52235670 | 52235774 | 52235694 | 52235694 | Missense_Mutation | A | T | p.T1069S |
| NMCG1_CENTRAL_NERVOUS_SYSTEM | 52240773 | 52240865 | 52240782 | 52240782 | Missense_Mutation | T | G | p.S1099A |
| OACM51_OESOPHAGUS | 52240773 | 52240865 | 52240816 | 52240816 | Missense_Mutation | G | A | p.R1110Q |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ITGA1 |
| 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 ITGA1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ITGA1 |
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RelatedDrugs for ITGA1 |
| 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 ITGA1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| ITGA1 | C0017639 | Gliosis | 1 | CTD_human |
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