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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 NECAB3 |
 Gene summary |
| Gene information | Gene symbol | NECAB3 | Gene ID | 63941 |
| Gene name | N-terminal EF-hand calcium binding protein 3 | |
| Synonyms | APBA2BP|EFCBP3|NIP1|STIP3|SYTIP2|XB51|dJ63M2.4|dJ63M2.5 | |
| Cytomap | 20q11.22 | |
| Type of gene | protein-coding | |
| Description | N-terminal EF-hand calcium-binding protein 3EF-hand calcium binding protein 3Nek2-interacting protein 1X11L-binding protein 51amyloid beta (A4) precursor protein-binding, family A, member 2 binding proteinamyloid beta A4 protein-binding family A memb | |
| Modification date | 20180523 | |
| UniProtAcc | Q96P71 | |
| Context | PubMed: NECAB3 [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 |
| NECAB3 | GO:0019538 | protein metabolic process | 12780348 |
| NECAB3 | GO:0042984 | regulation of amyloid precursor protein biosynthetic process | 10833507 |
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Exon skipping events across known transcript of Ensembl for NECAB3 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 NECAB3 |
| 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 NECAB3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_355945 | 20 | 32245595:32245663:32245747:32245839:32246282:32246360 | 32245747:32245839 | ENSG00000125967.12 | ENST00000488489.1,ENST00000477778.1,ENST00000485976.1,ENST00000606525.1,ENST00000478237.1,ENST00000246190.6,ENST00000485399.1,ENST00000375238.4,ENST00000494174.1,ENST00000483813.1 |
| exon_skip_355947 | 20 | 32245767:32245839:32246282:32246360:32246527:32246622 | 32246282:32246360 | ENSG00000125967.12 | ENST00000488489.1,ENST00000477778.1,ENST00000485976.1,ENST00000606525.1,ENST00000480994.1,ENST00000478237.1,ENST00000246190.6,ENST00000485399.1,ENST00000463246.1,ENST00000375238.4,ENST00000494174.1,ENST00000483813.1 |
| exon_skip_355952 | 20 | 32246527:32246640:32247302:32247356:32247458:32247538 | 32247302:32247356 | ENSG00000125967.12 | ENST00000488489.1,ENST00000606525.1,ENST00000480994.1,ENST00000478237.1,ENST00000607805.1,ENST00000485399.1,ENST00000375238.4,ENST00000494174.1 |
| exon_skip_355953 | 20 | 32246527:32246640:32247302:32247538:32247690:32247804 | 32247302:32247538 | ENSG00000125967.12 | ENST00000246190.6,ENST00000483813.1 |
| exon_skip_355954 | 20 | 32246527:32246640:32247458:32247538:32247690:32247804 | 32247458:32247538 | ENSG00000125967.12 | ENST00000485976.1,ENST00000463246.1,ENST00000439478.1 |
| exon_skip_355959 | 20 | 32248064:32248201:32250017:32250047:32251339:32251525 | 32250017:32250047 | ENSG00000125967.12 | ENST00000485976.1 |
| exon_skip_355961 | 20 | 32248064:32248201:32257180:32257278:32257492:32257518 | 32257180:32257278 | ENSG00000125967.12 | ENST00000488489.1,ENST00000607805.1,ENST00000246190.6,ENST00000485399.1,ENST00000375238.4,ENST00000493590.1,ENST00000606690.1,ENST00000439478.1 |
| exon_skip_355965 | 20 | 32257180:32257278:32257492:32257518:32258489:32258566 | 32257492:32257518 | ENSG00000125967.12 | ENST00000488489.1,ENST00000607805.1,ENST00000473892.1,ENST00000246190.6,ENST00000485399.1,ENST00000375238.4,ENST00000493590.1,ENST00000606690.1,ENST00000439478.1 |
| exon_skip_355970 | 20 | 32257492:32257518:32258019:32258227:32258489:32258566 | 32258019:32258227 | ENSG00000125967.12 | ENST00000606699.1 |
| exon_skip_355972 | 20 | 32257492:32257518:32258489:32258566:32260203:32260228 | 32258489:32258566 | ENSG00000125967.12 | ENST00000493590.1 |
| exon_skip_355974 | 20 | 32257492:32257518:32258489:32258587:32260203:32260228 | 32258489:32258587 | ENSG00000125967.12 | ENST00000488489.1 |
| exon_skip_355975 | 20 | 32257492:32257518:32258489:32258598:32260203:32260228 | 32258489:32258598 | ENSG00000125967.12 | ENST00000607805.1,ENST00000246190.6,ENST00000485399.1,ENST00000484824.2,ENST00000375238.4,ENST00000606690.1,ENST00000439478.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for NECAB3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_355945 | 20 | 32245595:32245663:32245747:32245839:32246282:32246360 | 32245747:32245839 | ENSG00000125967.12 | ENST00000477778.1,ENST00000246190.6,ENST00000375238.4,ENST00000606525.1,ENST00000488489.1,ENST00000483813.1,ENST00000485399.1,ENST00000485976.1,ENST00000478237.1,ENST00000494174.1 |
| exon_skip_355947 | 20 | 32245767:32245839:32246282:32246360:32246527:32246622 | 32246282:32246360 | ENSG00000125967.12 | ENST00000477778.1,ENST00000246190.6,ENST00000375238.4,ENST00000606525.1,ENST00000488489.1,ENST00000483813.1,ENST00000485399.1,ENST00000485976.1,ENST00000478237.1,ENST00000494174.1,ENST00000463246.1,ENST00000480994.1 |
| exon_skip_355952 | 20 | 32246527:32246640:32247302:32247356:32247458:32247538 | 32247302:32247356 | ENSG00000125967.12 | ENST00000375238.4,ENST00000606525.1,ENST00000488489.1,ENST00000485399.1,ENST00000478237.1,ENST00000494174.1,ENST00000480994.1,ENST00000607805.1 |
| exon_skip_355953 | 20 | 32246527:32246640:32247302:32247538:32247690:32247804 | 32247302:32247538 | ENSG00000125967.12 | ENST00000246190.6,ENST00000483813.1 |
| exon_skip_355954 | 20 | 32246527:32246640:32247458:32247538:32247690:32247804 | 32247458:32247538 | ENSG00000125967.12 | ENST00000485976.1,ENST00000463246.1,ENST00000439478.1 |
| exon_skip_355959 | 20 | 32248064:32248201:32250017:32250047:32251339:32251525 | 32250017:32250047 | ENSG00000125967.12 | ENST00000485976.1 |
| exon_skip_355961 | 20 | 32248064:32248201:32257180:32257278:32257492:32257518 | 32257180:32257278 | ENSG00000125967.12 | ENST00000246190.6,ENST00000375238.4,ENST00000488489.1,ENST00000485399.1,ENST00000606690.1,ENST00000439478.1,ENST00000607805.1,ENST00000493590.1 |
| exon_skip_355965 | 20 | 32257180:32257278:32257492:32257518:32258489:32258566 | 32257492:32257518 | ENSG00000125967.12 | ENST00000246190.6,ENST00000375238.4,ENST00000488489.1,ENST00000485399.1,ENST00000606690.1,ENST00000439478.1,ENST00000607805.1,ENST00000493590.1,ENST00000473892.1 |
| exon_skip_355970 | 20 | 32257492:32257518:32258019:32258227:32258489:32258566 | 32258019:32258227 | ENSG00000125967.12 | ENST00000606699.1 |
| exon_skip_355972 | 20 | 32257492:32257518:32258489:32258566:32260203:32260228 | 32258489:32258566 | ENSG00000125967.12 | ENST00000493590.1 |
| exon_skip_355974 | 20 | 32257492:32257518:32258489:32258587:32260203:32260228 | 32258489:32258587 | ENSG00000125967.12 | ENST00000488489.1 |
| exon_skip_355975 | 20 | 32257492:32257518:32258489:32258598:32260203:32260228 | 32258489:32258598 | ENSG00000125967.12 | ENST00000246190.6,ENST00000375238.4,ENST00000485399.1,ENST00000606690.1,ENST00000439478.1,ENST00000607805.1,ENST00000484824.2 |
| 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 NECAB3 |
| 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 |
| ENST00000246190 | 32245747 | 32245839 | Frame-shift |
| ENST00000246190 | 32247302 | 32247538 | Frame-shift |
| ENST00000246190 | 32257180 | 32257278 | Frame-shift |
| ENST00000246190 | 32257492 | 32257518 | Frame-shift |
| ENST00000246190 | 32258489 | 32258598 | Frame-shift |
| ENST00000246190 | 32246282 | 32246360 | 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 |
| ENST00000246190 | 32245747 | 32245839 | Frame-shift |
| ENST00000246190 | 32247302 | 32247538 | Frame-shift |
| ENST00000246190 | 32257180 | 32257278 | Frame-shift |
| ENST00000246190 | 32257492 | 32257518 | Frame-shift |
| ENST00000246190 | 32258489 | 32258598 | Frame-shift |
| ENST00000246190 | 32246282 | 32246360 | In-frame |
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Infer the effects of exon skipping event on protein functional features for NECAB3 |
| 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 |
| ENST00000246190 | 2006 | 396 | 32246282 | 32246360 | 1049 | 1126 | 331 | 356 |
| 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 |
| ENST00000246190 | 2006 | 396 | 32246282 | 32246360 | 1049 | 1126 | 331 | 356 |
| 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 NECAB3 |
| - 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. |
NECAB3_LUAD_exon_skip_355953_psi_boxplot.png |
NECAB3_PCPG_exon_skip_355953_psi_boxplot.png |
| - 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 |
| COAD | TCGA-AD-6889-01 | exon_skip_355945 | 32245748 | 32245839 | 32245750 | 32245750 | Frame_Shift_Del | G | - | p.P387fs |
| PRAD | TCGA-EJ-7785-01 | exon_skip_355945 | 32245748 | 32245839 | 32245753 | 32245753 | Frame_Shift_Del | A | - | p.F386fs |
| PCPG | TCGA-SP-A6QI-01 | exon_skip_355952 | 32247303 | 32247356 | 32247350 | 32247350 | Frame_Shift_Del | G | - | p.R278fs |
| PCPG | TCGA-SP-A6QI-01 | exon_skip_355953 | 32247303 | 32247538 | 32247350 | 32247350 | Frame_Shift_Del | G | - | p.R278fs |
| PCPG | TCGA-SP-A6QI-01 | exon_skip_355953 | 32247303 | 32247538 | 32247387 | 32247387 | Frame_Shift_Del | C | - | p.W265fs |
| KICH | TCGA-KN-8435-01 | exon_skip_355972 | 32258490 | 32258566 | 32258501 | 32258501 | Frame_Shift_Del | C | - | p.G84fs |
| KICH | TCGA-KN-8435-01 | exon_skip_355972 | 32258490 | 32258566 | 32258501 | 32258501 | Frame_Shift_Del | C | - | p.H85fs |
| KICH | TCGA-KN-8435-01 | exon_skip_355974 | 32258490 | 32258587 | 32258501 | 32258501 | Frame_Shift_Del | C | - | p.G84fs |
| KICH | TCGA-KN-8435-01 | exon_skip_355974 | 32258490 | 32258587 | 32258501 | 32258501 | Frame_Shift_Del | C | - | p.H85fs |
| KICH | TCGA-KN-8435-01 | exon_skip_355975 | 32258490 | 32258598 | 32258501 | 32258501 | Frame_Shift_Del | C | - | p.G84fs |
| KICH | TCGA-KN-8435-01 | exon_skip_355975 | 32258490 | 32258598 | 32258501 | 32258501 | Frame_Shift_Del | C | - | p.H85fs |
| LUAD | TCGA-44-2662-01 | exon_skip_355952 | 32247303 | 32247356 | 32247349 | 32247350 | Frame_Shift_Ins | - | G | p.A278fs |
| LUAD | TCGA-44-2662-01 | exon_skip_355953 | 32247303 | 32247538 | 32247349 | 32247350 | Frame_Shift_Ins | - | G | p.A278fs |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-44-2662-01 |
| Cancer type: LUAD | |
| ESID: exon_skip_355952 | |
| Skipped exon start: 32247303 | |
| Skipped exon end: 32247356 | |
| Mutation start: 32247349 | |
| Mutation end: 32247350 | |
| Mutation type: Frame_Shift_Ins | |
| Reference seq: - | |
| Mutation seq: G | |
| AAchange: p.A278fs | |
| Sample: TCGA-44-2662-01 |
| Cancer type: LUAD | |
| ESID: exon_skip_355953 | |
| Skipped exon start: 32247303 | |
| Skipped exon end: 32247538 | |
| Mutation start: 32247349 | |
| Mutation end: 32247350 | |
| Mutation type: Frame_Shift_Ins | |
| Reference seq: - | |
| Mutation seq: G | |
| AAchange: p.A278fs | |
exon_skip_355953_LUAD_TCGA-44-2662-01.png | |
exon_skip_425876_LUAD_TCGA-44-2662-01.png | |
exon_skip_93891_LUAD_TCGA-44-2662-01.png | |
 | Sample: TCGA-SP-A6QI-01 |
| Cancer type: PCPG | |
| ESID: exon_skip_355952 | |
| Skipped exon start: 32247303 | |
| Skipped exon end: 32247356 | |
| Mutation start: 32247350 | |
| Mutation end: 32247350 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: G | |
| Mutation seq: - | |
| AAchange: p.R278fs | |
| Sample: TCGA-SP-A6QI-01 |
| Cancer type: PCPG | |
| ESID: exon_skip_355953 | |
| Skipped exon start: 32247303 | |
| Skipped exon end: 32247538 | |
| Mutation start: 32247350 | |
| Mutation end: 32247350 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: G | |
| Mutation seq: - | |
| AAchange: p.R278fs | |
| Sample: TCGA-SP-A6QI-01 |
| Cancer type: PCPG | |
| ESID: exon_skip_355953 | |
| Skipped exon start: 32247303 | |
| Skipped exon end: 32247538 | |
| Mutation start: 32247387 | |
| Mutation end: 32247387 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: C | |
| Mutation seq: - | |
| AAchange: p.W265fs | |
exon_skip_337625_PCPG_TCGA-SP-A6QI-01.png | |
exon_skip_355953_PCPG_TCGA-SP-A6QI-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 |
| HGC27_STOMACH | 32245748 | 32245839 | 32245793 | 32245793 | Missense_Mutation | C | T | p.D373N |
| MDAMB435S_SKIN | 32245748 | 32245839 | 32245826 | 32245826 | Missense_Mutation | G | A | p.P362S |
| GOTO_AUTONOMIC_GANGLIA | 32245748 | 32245839 | 32245828 | 32245828 | Missense_Mutation | G | A | p.S361L |
| SNU1040_LARGE_INTESTINE | 32246283 | 32246360 | 32246353 | 32246353 | Missense_Mutation | C | T | p.A334T |
| SKMM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32247303 | 32247356 | 32247349 | 32247349 | Missense_Mutation | C | T | p.R278Q |
| SKMM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32247303 | 32247538 | 32247349 | 32247349 | Missense_Mutation | C | T | p.R278Q |
| MM370_SKIN | 32247303 | 32247538 | 32247377 | 32247378 | Missense_Mutation | GG | TA | p.P269T |
| ACCMESO1_PLEURA | 32247303 | 32247538 | 32247409 | 32247409 | Missense_Mutation | G | A | p.P258L |
| GP5D_LARGE_INTESTINE | 32247303 | 32247538 | 32247449 | 32247449 | Missense_Mutation | C | T | p.V245M |
| SNU1040_LARGE_INTESTINE | 32247459 | 32247538 | 32247493 | 32247493 | Missense_Mutation | C | T | p.R230H |
| SNU1040_LARGE_INTESTINE | 32247303 | 32247538 | 32247493 | 32247493 | Missense_Mutation | C | T | p.R230H |
| SNU1040_LARGE_INTESTINE | 32247459 | 32247538 | 32247535 | 32247535 | Missense_Mutation | C | T | p.R216H |
| SNU1040_LARGE_INTESTINE | 32247303 | 32247538 | 32247535 | 32247535 | Missense_Mutation | C | T | p.R216H |
| RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32257493 | 32257518 | 32257496 | 32257496 | Missense_Mutation | A | T | p.C96S |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32258490 | 32258566 | 32258497 | 32258497 | Missense_Mutation | G | A | p.L86F |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32258490 | 32258587 | 32258497 | 32258497 | Missense_Mutation | G | A | p.L86F |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32258490 | 32258598 | 32258497 | 32258497 | Missense_Mutation | G | A | p.L86F |
| HEC6_ENDOMETRIUM | 32245748 | 32245839 | 32245748 | 32245748 | Splice_Site | C | A | p.A388S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NECAB3 |
| 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 NECAB3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NECAB3 |
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RelatedDrugs for NECAB3 |
| 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 NECAB3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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