|
||||||
|
 | |
| |
| |
| |
| 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 ITGAM |
 Gene summary |
| Gene information | Gene symbol | ITGAM | Gene ID | 3684 |
| Gene name | integrin subunit alpha M | |
| Synonyms | CD11B|CR3A|MAC-1|MAC1A|MO1A|SLEB6 | |
| Cytomap | 16p11.2 | |
| Type of gene | protein-coding | |
| Description | integrin alpha-MCD11 antigen-like family member BCR-3 alpha chainantigen CD11b (p170)cell surface glycoprotein MAC-1 subunit alphacomplement component 3 receptor 3 subunitintegrin, alpha M (complement component 3 receptor 3 subunit)leukocyte adhesi | |
| Modification date | 20180527 | |
| UniProtAcc | P11215 | |
| Context | PubMed: ITGAM [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 ITGAM 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 ITGAM |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for ITGAM |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_136042 | 16 | 31277350:31277468:31282274:31282405:31283167:31283313 | 31282274:31282405 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| exon_skip_136044 | 16 | 31282274:31282405:31283167:31283313:31284685:31284839 | 31283167:31283313 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| exon_skip_136046 | 16 | 31288240:31288370:31289287:31289430:31308834:31308948 | 31289287:31289430 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| exon_skip_136047 | 16 | 31308834:31308975:31309062:31309275:31332561:31332692 | 31309062:31309275 | ENSG00000169896.12 | ENST00000544665.3 |
| exon_skip_136048 | 16 | 31308834:31308975:31309065:31309275:31332561:31332692 | 31309065:31309275 | ENSG00000169896.12 | ENST00000287497.8 |
| exon_skip_136050 | 16 | 31309065:31309275:31332561:31332692:31332784:31332948 | 31332561:31332692 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| exon_skip_136051 | 16 | 31340548:31340624:31341118:31341226:31341401:31341485 | 31341118:31341226 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for ITGAM |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_136042 | 16 | 31277350:31277468:31282274:31282405:31283167:31283313 | 31282274:31282405 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| exon_skip_136044 | 16 | 31282274:31282405:31283167:31283313:31284685:31284839 | 31283167:31283313 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| exon_skip_136046 | 16 | 31288240:31288370:31289287:31289430:31308834:31308948 | 31289287:31289430 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| exon_skip_136047 | 16 | 31308834:31308975:31309062:31309275:31332561:31332692 | 31309062:31309275 | ENSG00000169896.12 | ENST00000544665.3 |
| exon_skip_136048 | 16 | 31308834:31308975:31309065:31309275:31332561:31332692 | 31309065:31309275 | ENSG00000169896.12 | ENST00000287497.8 |
| exon_skip_136050 | 16 | 31309065:31309275:31332561:31332692:31332784:31332948 | 31332561:31332692 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| exon_skip_136051 | 16 | 31340548:31340624:31341118:31341226:31341401:31341485 | 31341118:31341226 | ENSG00000169896.12 | ENST00000287497.8,ENST00000544665.3 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for ITGAM |
| 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 |
| ENST00000287497 | 31282274 | 31282405 | Frame-shift |
| ENST00000287497 | 31283167 | 31283313 | Frame-shift |
| ENST00000287497 | 31289287 | 31289430 | Frame-shift |
| ENST00000287497 | 31332561 | 31332692 | Frame-shift |
| ENST00000287497 | 31309065 | 31309275 | In-frame |
| ENST00000287497 | 31341118 | 31341226 | 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 |
| ENST00000287497 | 31282274 | 31282405 | Frame-shift |
| ENST00000287497 | 31283167 | 31283313 | Frame-shift |
| ENST00000287497 | 31289287 | 31289430 | Frame-shift |
| ENST00000287497 | 31332561 | 31332692 | Frame-shift |
| ENST00000287497 | 31309065 | 31309275 | In-frame |
| ENST00000287497 | 31341118 | 31341226 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for ITGAM |
| 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 |
| ENST00000287497 | 3612 | 1152 | 31309065 | 31309275 | 1573 | 1782 | 499 | 569 |
| ENST00000287497 | 3612 | 1152 | 31341118 | 31341226 | 2944 | 3051 | 956 | 992 |
| 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 |
| ENST00000287497 | 3612 | 1152 | 31309065 | 31309275 | 1573 | 1782 | 499 | 569 |
| ENST00000287497 | 3612 | 1152 | 31341118 | 31341226 | 2944 | 3051 | 956 | 992 |
| 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 |
| P11215 | 499 | 569 | 499 | 499 | Alternative sequence | ID=VSP_047365;Note=In isoform 2. G->GQ;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:2457584,ECO:0000303|PubMed:2563162;Dbxref=PMID:2457584,PMID:2563162 |
| P11215 | 499 | 569 | 529 | 537 | Calcium binding | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P11215 | 499 | 569 | 17 | 1152 | Chain | ID=PRO_0000016289;Note=Integrin alpha-M |
| P11215 | 499 | 569 | 443 | 503 | Repeat | Note=FG-GAP 5;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00803 |
| P11215 | 499 | 569 | 506 | 564 | Repeat | Note=FG-GAP 6;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00803 |
| P11215 | 499 | 569 | 569 | 629 | Repeat | Note=FG-GAP 7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00803 |
| P11215 | 499 | 569 | 17 | 1104 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P11215 | 956 | 992 | 17 | 1152 | Chain | ID=PRO_0000016289;Note=Integrin alpha-M |
| P11215 | 956 | 992 | 978 | 978 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P11215 | 956 | 992 | 965 | 965 | Sequence conflict | Note=L->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P11215 | 956 | 992 | 17 | 1104 | 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 |
| P11215 | 499 | 569 | 499 | 499 | Alternative sequence | ID=VSP_047365;Note=In isoform 2. G->GQ;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:2457584,ECO:0000303|PubMed:2563162;Dbxref=PMID:2457584,PMID:2563162 |
| P11215 | 499 | 569 | 529 | 537 | Calcium binding | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P11215 | 499 | 569 | 17 | 1152 | Chain | ID=PRO_0000016289;Note=Integrin alpha-M |
| P11215 | 499 | 569 | 443 | 503 | Repeat | Note=FG-GAP 5;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00803 |
| P11215 | 499 | 569 | 506 | 564 | Repeat | Note=FG-GAP 6;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00803 |
| P11215 | 499 | 569 | 569 | 629 | Repeat | Note=FG-GAP 7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00803 |
| P11215 | 499 | 569 | 17 | 1104 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P11215 | 956 | 992 | 17 | 1152 | Chain | ID=PRO_0000016289;Note=Integrin alpha-M |
| P11215 | 956 | 992 | 978 | 978 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P11215 | 956 | 992 | 965 | 965 | Sequence conflict | Note=L->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P11215 | 956 | 992 | 17 | 1104 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
SNVs in the skipped exons for ITGAM |
| - 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-A39Y-01 | exon_skip_136044 | 31283168 | 31283313 | 31283222 | 31283222 | Frame_Shift_Del | T | - | p.F205fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_136046 | 31289288 | 31289430 | 31289316 | 31289316 | Frame_Shift_Del | C | - | p.N414fs |
| LIHC | TCGA-DD-AAEH-01 | exon_skip_136046 | 31289288 | 31289430 | 31289337 | 31289337 | Frame_Shift_Del | G | - | p.L421fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_136047 exon_skip_136048 | 31309063 | 31309275 | 31309099 | 31309099 | Frame_Shift_Del | G | - | p.G512fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_136047 exon_skip_136048 | 31309066 | 31309275 | 31309099 | 31309099 | Frame_Shift_Del | G | - | p.G512fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_136051 | 31341119 | 31341226 | 31341145 | 31341145 | Frame_Shift_Del | C | - | p.L966fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_136051 | 31341119 | 31341226 | 31341205 | 31341205 | Frame_Shift_Del | C | - | p.R986fs |
| UCEC | TCGA-AP-A0LT-01 | exon_skip_136051 | 31341119 | 31341226 | 31341205 | 31341205 | Frame_Shift_Del | C | - | p.R986fs |
| BLCA | TCGA-FD-A6TE-01 | exon_skip_136042 | 31282275 | 31282405 | 31282368 | 31282368 | Nonsense_Mutation | C | G | p.S174* |
| CESC | TCGA-C5-A1BJ-01 | exon_skip_136042 | 31282275 | 31282405 | 31282368 | 31282368 | Nonsense_Mutation | C | G | p.S174* |
| SKCM | TCGA-EE-A2GO-06 | exon_skip_136044 | 31283168 | 31283313 | 31283225 | 31283225 | Nonsense_Mutation | C | T | p.Q206* |
| PRAD | TCGA-ZG-A9LM-01 | exon_skip_136046 | 31289288 | 31289430 | 31289353 | 31289353 | Nonsense_Mutation | C | T | p.Q427* |
| - 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 |
| EN_ENDOMETRIUM | 31309063 | 31309275 | 31309149 | 31309149 | Frame_Shift_Del | G | - | p.L527fs |
| EN_ENDOMETRIUM | 31309066 | 31309275 | 31309149 | 31309149 | Frame_Shift_Del | G | - | p.L527fs |
| HEP3B217_LIVER | 31282275 | 31282405 | 31282280 | 31282281 | Missense_Mutation | CC | AA | p.P145N |
| C84_LARGE_INTESTINE | 31289288 | 31289430 | 31289299 | 31289299 | Missense_Mutation | G | A | p.A409T |
| P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31289288 | 31289430 | 31289299 | 31289299 | Missense_Mutation | G | A | p.A409T |
| SNU1040_LARGE_INTESTINE | 31289288 | 31289430 | 31289299 | 31289299 | Missense_Mutation | G | A | p.A409T |
| K562_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31289288 | 31289430 | 31289311 | 31289311 | Missense_Mutation | C | T | p.R413W |
| SW684_SOFT_TISSUE | 31289288 | 31289430 | 31289312 | 31289312 | Missense_Mutation | G | A | p.R413Q |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31289288 | 31289430 | 31289362 | 31289362 | Missense_Mutation | G | A | p.G430S |
| HT55_LARGE_INTESTINE | 31289288 | 31289430 | 31289380 | 31289380 | Missense_Mutation | A | T | p.R436W |
| NCIH250_LUNG | 31309063 | 31309275 | 31309208 | 31309208 | Missense_Mutation | A | T | p.D547V |
| NCIH250_LUNG | 31309066 | 31309275 | 31309208 | 31309208 | Missense_Mutation | A | T | p.D547V |
| NCIH23_LUNG | 31332562 | 31332692 | 31332587 | 31332587 | Missense_Mutation | C | A | p.P578H |
| EN_ENDOMETRIUM | 31332562 | 31332692 | 31332587 | 31332587 | Missense_Mutation | C | A | p.P578H |
| NCIH23_LUNG | 31332562 | 31332692 | 31332587 | 31332588 | Missense_Mutation | CC | AA | p.P578Q |
| SNU81_LARGE_INTESTINE | 31332562 | 31332692 | 31332652 | 31332652 | Missense_Mutation | G | T | p.D600Y |
| NCIH23_LUNG | 31332562 | 31332692 | 31332673 | 31332673 | Missense_Mutation | G | A | p.G607R |
| NCIH630_LARGE_INTESTINE | 31341119 | 31341226 | 31341173 | 31341173 | Missense_Mutation | G | A | p.V975I |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31341119 | 31341226 | 31341204 | 31341204 | Missense_Mutation | G | A | p.R985H |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31309063 | 31309275 | 31309275 | 31309275 | Splice_Site | G | T | p.Q569H |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 31309066 | 31309275 | 31309275 | 31309275 | Splice_Site | G | T | p.Q569H |
| HEC6_ENDOMETRIUM | 31332562 | 31332692 | 31332563 | 31332563 | Splice_Site | G | A | p.R570Q |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ITGAM |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ITGAM |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ITGAM |
Top |
RelatedDrugs for ITGAM |
| 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 ITGAM |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| ITGAM | C0024141 | Lupus Erythematosus, Systemic | 2 | CTD_human |
| ITGAM | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| ITGAM | C0020877 | Ileitis | 1 | CTD_human |
| ITGAM | C0023487 | Acute Promyelocytic Leukemia | 1 | CTD_human |
| ITGAM | C0036341 | Schizophrenia | 1 | PSYGENET |
| ITGAM | C0162820 | Dermatitis, Allergic Contact | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|