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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 NDC1 |
 Gene summary |
| Gene information | Gene symbol | NDC1 | Gene ID | 55706 |
| Gene name | NDC1 transmembrane nucleoporin | |
| Synonyms | NET3|TMEM48 | |
| Cytomap | 1p32.3 | |
| Type of gene | protein-coding | |
| Description | nucleoporin NDC1nuclear division cycle 1 homologtransmembrane protein 48 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9BTX1 | |
| Context | PubMed: NDC1 [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 NDC1 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 NDC1 |
| 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 NDC1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_27225 | 1 | 54233562:54233706:54238001:54238162:54252830:54252931 | 54238001:54238162 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27226 | 1 | 54238001:54238162:54252830:54252931:54254805:54254869 | 54252830:54252931 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27232 | 1 | 54252830:54252931:54254805:54254869:54258901:54258952 | 54254805:54254869 | ENSG00000058804.10 | ENST00000371429.3,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27235 | 1 | 54254805:54254869:54258901:54258952:54262361:54262428 | 54258901:54258952 | ENSG00000058804.10 | ENST00000371429.3,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27243 | 1 | 54258901:54258952:54262361:54262477:54262571:54262817 | 54262361:54262477 | ENSG00000058804.10 | ENST00000371429.3,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27251 | 1 | 54262420:54262477:54262571:54262817:54266365:54266521 | 54262571:54262817 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27252 | 1 | 54262571:54262817:54266365:54266521:54269600:54269682 | 54266365:54266521 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27253 | 1 | 54266365:54266521:54269600:54269682:54272097:54272190 | 54269600:54269682 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27254 | 1 | 54269600:54269682:54272097:54272190:54273328:54273464 | 54272097:54272190 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000234725.8 |
| exon_skip_27255 | 1 | 54272097:54272190:54273328:54273464:54275367:54275419 | 54273328:54273464 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000234725.8 |
| exon_skip_27256 | 1 | 54273328:54273464:54275367:54275419:54284643:54284752 | 54275367:54275419 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000234725.8 |
| exon_skip_27260 | 1 | 54291470:54291609:54293671:54293846:54298162:54298264 | 54293671:54293846 | ENSG00000058804.10 | ENST00000480952.1,ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27262 | 1 | 54293671:54293846:54298162:54298264:54301172:54301293 | 54298162:54298264 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1 |
| exon_skip_27263 | 1 | 54298162:54298264:54301172:54301293:54303877:54303940 | 54301172:54301293 | ENSG00000058804.10 | ENST00000540001.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for NDC1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_27225 | 1 | 54233562:54233706:54238001:54238162:54252830:54252931 | 54238001:54238162 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27226 | 1 | 54238001:54238162:54252830:54252931:54254805:54254869 | 54252830:54252931 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27232 | 1 | 54252830:54252931:54254805:54254869:54258901:54258952 | 54254805:54254869 | ENSG00000058804.10 | ENST00000371429.3,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27235 | 1 | 54254805:54254869:54258901:54258952:54262361:54262428 | 54258901:54258952 | ENSG00000058804.10 | ENST00000371429.3,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27243 | 1 | 54258901:54258952:54262361:54262477:54262571:54262817 | 54262361:54262477 | ENSG00000058804.10 | ENST00000371429.3,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27251 | 1 | 54262420:54262477:54262571:54262817:54266365:54266521 | 54262571:54262817 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27252 | 1 | 54262571:54262817:54266365:54266521:54269600:54269682 | 54266365:54266521 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27253 | 1 | 54266365:54266521:54269600:54269682:54272097:54272190 | 54269600:54269682 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8 |
| exon_skip_27254 | 1 | 54269600:54269682:54272097:54272190:54273328:54273464 | 54272097:54272190 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000234725.8 |
| exon_skip_27255 | 1 | 54272097:54272190:54273328:54273464:54275367:54275419 | 54273328:54273464 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000234725.8 |
| exon_skip_27256 | 1 | 54273328:54273464:54275367:54275419:54284643:54284752 | 54275367:54275419 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000234725.8 |
| exon_skip_27260 | 1 | 54291470:54291609:54293671:54293846:54298162:54298264 | 54293671:54293846 | ENSG00000058804.10 | ENST00000371429.3,ENST00000540001.1,ENST00000537333.1,ENST00000234725.8,ENST00000480952.1 |
| exon_skip_27263 | 1 | 54298162:54298264:54301172:54301293:54303877:54303940 | 54301172:54301293 | ENSG00000058804.10 | ENST00000540001.1 |
| 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 NDC1 |
| 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 |
| ENST00000371429 | 54238001 | 54238162 | Frame-shift |
| ENST00000371429 | 54252830 | 54252931 | Frame-shift |
| ENST00000371429 | 54254805 | 54254869 | Frame-shift |
| ENST00000371429 | 54262361 | 54262477 | Frame-shift |
| ENST00000371429 | 54269600 | 54269682 | Frame-shift |
| ENST00000371429 | 54273328 | 54273464 | Frame-shift |
| ENST00000371429 | 54275367 | 54275419 | Frame-shift |
| ENST00000371429 | 54293671 | 54293846 | Frame-shift |
| ENST00000371429 | 54258901 | 54258952 | In-frame |
| ENST00000371429 | 54262571 | 54262817 | In-frame |
| ENST00000371429 | 54266365 | 54266521 | In-frame |
| ENST00000371429 | 54272097 | 54272190 | In-frame |
| ENST00000371429 | 54298162 | 54298264 | 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 |
| ENST00000371429 | 54238001 | 54238162 | Frame-shift |
| ENST00000371429 | 54252830 | 54252931 | Frame-shift |
| ENST00000371429 | 54254805 | 54254869 | Frame-shift |
| ENST00000371429 | 54262361 | 54262477 | Frame-shift |
| ENST00000371429 | 54269600 | 54269682 | Frame-shift |
| ENST00000371429 | 54273328 | 54273464 | Frame-shift |
| ENST00000371429 | 54275367 | 54275419 | Frame-shift |
| ENST00000371429 | 54293671 | 54293846 | Frame-shift |
| ENST00000371429 | 54258901 | 54258952 | In-frame |
| ENST00000371429 | 54262571 | 54262817 | In-frame |
| ENST00000371429 | 54266365 | 54266521 | In-frame |
| ENST00000371429 | 54272097 | 54272190 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NDC1 |
| 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 |
| ENST00000371429 | 5151 | 674 | 54298162 | 54298264 | 778 | 879 | 59 | 93 |
| ENST00000371429 | 5151 | 674 | 54272097 | 54272190 | 1491 | 1583 | 297 | 328 |
| ENST00000371429 | 5151 | 674 | 54266365 | 54266521 | 1666 | 1821 | 355 | 407 |
| ENST00000371429 | 5151 | 674 | 54262571 | 54262817 | 1822 | 2067 | 407 | 489 |
| ENST00000371429 | 5151 | 674 | 54258901 | 54258952 | 2184 | 2234 | 528 | 545 |
| 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 |
| ENST00000371429 | 5151 | 674 | 54272097 | 54272190 | 1491 | 1583 | 297 | 328 |
| ENST00000371429 | 5151 | 674 | 54266365 | 54266521 | 1666 | 1821 | 355 | 407 |
| ENST00000371429 | 5151 | 674 | 54262571 | 54262817 | 1822 | 2067 | 407 | 489 |
| ENST00000371429 | 5151 | 674 | 54258901 | 54258952 | 2184 | 2234 | 528 | 545 |
| 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 NDC1 |
| - 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 |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_27225 | 54238002 | 54238162 | 54238078 | 54238078 | Frame_Shift_Del | T | - | p.T629fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_27251 | 54262572 | 54262817 | 54262651 | 54262651 | Frame_Shift_Del | A | - | p.F463fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_27262 | 54298163 | 54298264 | 54298258 | 54298258 | Frame_Shift_Del | A | - | p.F62fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_27251 | 54262572 | 54262817 | 54262791 | 54262792 | Frame_Shift_Ins | - | T | p.N*416fs |
| BLCA | TCGA-XF-A9T5-01 | exon_skip_27251 | 54262572 | 54262817 | 54262803 | 54262803 | Nonsense_Mutation | G | A | p.Q413* |
| - 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 |
| LS411N_LARGE_INTESTINE | 54262572 | 54262817 | 54262597 | 54262597 | Frame_Shift_Del | C | - | p.G481fs |
| JAR_PLACENTA | 54238002 | 54238162 | 54238081 | 54238082 | Frame_Shift_Ins | - | A | p.K628fs |
| RKO_LARGE_INTESTINE | 54258902 | 54258952 | 54258908 | 54258909 | Frame_Shift_Ins | - | A | p.F543fs |
| RL952_ENDOMETRIUM | 54298163 | 54298264 | 54298189 | 54298190 | In_Frame_Ins | - | TTA | p.84_85insI |
| KYSE70_OESOPHAGUS | 54238002 | 54238162 | 54238017 | 54238017 | Missense_Mutation | A | T | p.F649Y |
| ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 54238002 | 54238162 | 54238017 | 54238017 | Missense_Mutation | A | T | p.F649Y |
| NCIH3255_LUNG | 54238002 | 54238162 | 54238037 | 54238037 | Missense_Mutation | G | C | p.I642M |
| FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 54238002 | 54238162 | 54238050 | 54238050 | Missense_Mutation | A | G | p.L638P |
| CORL47_LUNG | 54238002 | 54238162 | 54238128 | 54238128 | Missense_Mutation | G | A | p.S612F |
| UWB1289_OVARY | 54238002 | 54238162 | 54238141 | 54238141 | Missense_Mutation | G | A | p.L608F |
| GMEL_SKIN | 54252831 | 54252931 | 54252842 | 54252842 | Missense_Mutation | T | C | p.T597A |
| CW2_LARGE_INTESTINE | 54254806 | 54254869 | 54254815 | 54254815 | Missense_Mutation | C | T | p.A564T |
| GP2D_LARGE_INTESTINE | 54262572 | 54262817 | 54262722 | 54262722 | Missense_Mutation | T | C | p.T440A |
| SNU489_CENTRAL_NERVOUS_SYSTEM | 54266366 | 54266521 | 54266462 | 54266462 | Missense_Mutation | T | C | p.M376V |
| HEC251_ENDOMETRIUM | 54266366 | 54266521 | 54266474 | 54266474 | Missense_Mutation | G | T | p.L372I |
| UMUC14_URINARY_TRACT | 54269601 | 54269682 | 54269612 | 54269612 | Missense_Mutation | A | T | p.L352H |
| HEC108_ENDOMETRIUM | 54272098 | 54272190 | 54272138 | 54272138 | Missense_Mutation | A | G | p.L315P |
| SNU1040_LARGE_INTESTINE | 54273329 | 54273464 | 54273331 | 54273331 | Missense_Mutation | C | T | p.E297K |
| NCIH1355_LUNG | 54273329 | 54273464 | 54273442 | 54273442 | Missense_Mutation | T | C | p.T260A |
| MDAMB361_BREAST | 54273329 | 54273464 | 54273457 | 54273457 | Missense_Mutation | G | A | p.H255Y |
| HCT116_LARGE_INTESTINE | 54275368 | 54275419 | 54275396 | 54275396 | Missense_Mutation | T | G | p.S243R |
| HT115_LARGE_INTESTINE | 54275368 | 54275419 | 54275399 | 54275399 | Missense_Mutation | T | C | p.I242V |
| BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 54275368 | 54275419 | 54275400 | 54275400 | Missense_Mutation | C | A | p.W241C |
| CME1_SOFT_TISSUE | 54301173 | 54301293 | 54301190 | 54301190 | Missense_Mutation | G | C | p.P54R |
| ESS1_ENDOMETRIUM | 54301173 | 54301293 | 54301245 | 54301245 | Missense_Mutation | G | T | p.L36I |
| HCC1599_MATCHED_NORMAL_TISSUE | 54301173 | 54301293 | 54301277 | 54301277 | Missense_Mutation | A | C | p.I25R |
| SNU81_LARGE_INTESTINE | 54262572 | 54262817 | 54262815 | 54262815 | Nonsense_Mutation | C | A | p.E409* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NDC1 |
| 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 NDC1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NDC1 |
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RelatedDrugs for NDC1 |
| 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 NDC1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| NDC1 | C0043094 | Weight Gain | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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