|
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 REG4 |
Gene summary |
Gene information | Gene symbol | REG4 | Gene ID | 83998 |
Gene name | regenerating family member 4 | |
Synonyms | GISP|REG-IV|RELP | |
Cytomap | 1p12 | |
Type of gene | protein-coding | |
Description | regenerating islet-derived protein 4REG-4REG-like proteingastrointestinal secretory proteinreg IVregenerating gene type IVregenerating islet-derived family, member 4regenerating islet-derived protein IV | |
Modification date | 20180523 | |
UniProtAcc | Q9BYZ8 | |
Context | PubMed: REG4 [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 REG4 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 REG4 |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
Top |
Exon skipping events with PSIs in TCGA for REG4 |
Information of exkip skipping event in TCGA. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_29745 | 1 | 120337099:120337308:120341119:120341225:120342347:120342485 | 120341119:120341225 | ENSG00000134193.10 | ENST00000354219.1,ENST00000256585.5 |
exon_skip_29747 | 1 | 120337035:120337308:120342347:120342485:120345690:120345788 | 120342347:120342485 | ENSG00000134193.10 | ENST00000530654.1 |
exon_skip_29748 | 1 | 120341119:120341225:120342347:120342485:120345690:120345788 | 120342347:120342485 | ENSG00000134193.10 | ENST00000354219.1,ENST00000256585.5 |
exon_skip_29753 | 1 | 120345690:120345788:120351325:120351486:120354031:120354203 | 120351325:120351486 | ENSG00000134193.10 | ENST00000256585.5,ENST00000369401.4 |
PSI values of skipped exons in TCGA. |
Top |
Exon skipping events with PSIs in GTEx for REG4 |
Information of exkip skipping event in GTEx |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_29745 | 1 | 120337099:120337308:120341119:120341225:120342347:120342485 | 120341119:120341225 | ENSG00000134193.10 | ENST00000354219.1,ENST00000256585.5 |
exon_skip_29747 | 1 | 120337035:120337308:120342347:120342485:120345690:120345788 | 120342347:120342485 | ENSG00000134193.10 | ENST00000530654.1 |
exon_skip_29748 | 1 | 120341119:120341225:120342347:120342485:120345690:120345788 | 120342347:120342485 | ENSG00000134193.10 | ENST00000354219.1,ENST00000256585.5 |
exon_skip_29753 | 1 | 120345690:120345788:120351325:120351486:120354031:120354203 | 120351325:120351486 | ENSG00000134193.10 | ENST00000256585.5,ENST00000369401.4 |
PSI values of skipped exons in GTEx. |
* Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for REG4 |
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 |
ENST00000256585 | 120351325 | 120351486 | 3UTR-3CDS |
ENST00000256585 | 120341119 | 120341225 | Frame-shift |
ENST00000354219 | 120341119 | 120341225 | Frame-shift |
ENST00000256585 | 120342347 | 120342485 | In-frame |
ENST00000354219 | 120342347 | 120342485 | 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 |
ENST00000256585 | 120351325 | 120351486 | 3UTR-3CDS |
ENST00000256585 | 120341119 | 120341225 | Frame-shift |
ENST00000354219 | 120341119 | 120341225 | Frame-shift |
ENST00000256585 | 120342347 | 120342485 | In-frame |
ENST00000354219 | 120342347 | 120342485 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for REG4 |
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 |
ENST00000256585 | 1374 | 158 | 120342347 | 120342485 | 512 | 649 | 55 | 101 |
ENST00000354219 | 1534 | 158 | 120342347 | 120342485 | 606 | 743 | 55 | 101 |
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 |
ENST00000256585 | 1374 | 158 | 120342347 | 120342485 | 512 | 649 | 55 | 101 |
ENST00000354219 | 1534 | 158 | 120342347 | 120342485 | 606 | 743 | 55 | 101 |
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 |
Q9BYZ8 | 55 | 101 | 56 | 134 | Alternative sequence | ID=VSP_014305;Note=In isoform 2. LECQSYGNGAHLASILSLKEASTIAEYISGYQRSQPIWIGLHDPQKRQQWQWIDGAMYLYRSWSGKSMGGNKHCAEMSS->VRNLLPAWPGLSRAKDQPEPQISFDSGSSVLPGHYEEKPLWLVKWREEGCVFNSFNSVSIAEAGAVCQTLDGLQAHTDT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1281900 |
Q9BYZ8 | 55 | 101 | 56 | 134 | Alternative sequence | ID=VSP_014305;Note=In isoform 2. LECQSYGNGAHLASILSLKEASTIAEYISGYQRSQPIWIGLHDPQKRQQWQWIDGAMYLYRSWSGKSMGGNKHCAEMSS->VRNLLPAWPGLSRAKDQPEPQISFDSGSSVLPGHYEEKPLWLVKWREEGCVFNSFNSVSIAEAGAVCQTLDGLQAHTDT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1281900 |
Q9BYZ8 | 55 | 101 | 62 | 64 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 62 | 64 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 95 | 97 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 95 | 97 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 99 | 103 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 99 | 103 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 23 | 158 | Chain | ID=PRO_0000017437;Note=Regenerating islet-derived protein 4 |
Q9BYZ8 | 55 | 101 | 23 | 158 | Chain | ID=PRO_0000017437;Note=Regenerating islet-derived protein 4 |
Q9BYZ8 | 55 | 101 | 58 | 154 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00040,ECO:0000269|PubMed:20692269;Dbxref=PMID:20692269 |
Q9BYZ8 | 55 | 101 | 58 | 154 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00040,ECO:0000269|PubMed:20692269;Dbxref=PMID:20692269 |
Q9BYZ8 | 55 | 101 | 37 | 155 | Domain | Note=C-type lectin;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00040 |
Q9BYZ8 | 55 | 101 | 37 | 155 | Domain | Note=C-type lectin;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00040 |
Q9BYZ8 | 55 | 101 | 51 | 59 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 51 | 59 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 73 | 83 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 73 | 83 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 98 | 103 | Region | Note=Carbohydrate-binding |
Q9BYZ8 | 55 | 101 | 98 | 103 | Region | Note=Carbohydrate-binding |
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 |
Q9BYZ8 | 55 | 101 | 56 | 134 | Alternative sequence | ID=VSP_014305;Note=In isoform 2. LECQSYGNGAHLASILSLKEASTIAEYISGYQRSQPIWIGLHDPQKRQQWQWIDGAMYLYRSWSGKSMGGNKHCAEMSS->VRNLLPAWPGLSRAKDQPEPQISFDSGSSVLPGHYEEKPLWLVKWREEGCVFNSFNSVSIAEAGAVCQTLDGLQAHTDT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1281900 |
Q9BYZ8 | 55 | 101 | 56 | 134 | Alternative sequence | ID=VSP_014305;Note=In isoform 2. LECQSYGNGAHLASILSLKEASTIAEYISGYQRSQPIWIGLHDPQKRQQWQWIDGAMYLYRSWSGKSMGGNKHCAEMSS->VRNLLPAWPGLSRAKDQPEPQISFDSGSSVLPGHYEEKPLWLVKWREEGCVFNSFNSVSIAEAGAVCQTLDGLQAHTDT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1281900 |
Q9BYZ8 | 55 | 101 | 62 | 64 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 62 | 64 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 95 | 97 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 95 | 97 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 99 | 103 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 99 | 103 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 23 | 158 | Chain | ID=PRO_0000017437;Note=Regenerating islet-derived protein 4 |
Q9BYZ8 | 55 | 101 | 23 | 158 | Chain | ID=PRO_0000017437;Note=Regenerating islet-derived protein 4 |
Q9BYZ8 | 55 | 101 | 58 | 154 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00040,ECO:0000269|PubMed:20692269;Dbxref=PMID:20692269 |
Q9BYZ8 | 55 | 101 | 58 | 154 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00040,ECO:0000269|PubMed:20692269;Dbxref=PMID:20692269 |
Q9BYZ8 | 55 | 101 | 37 | 155 | Domain | Note=C-type lectin;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00040 |
Q9BYZ8 | 55 | 101 | 37 | 155 | Domain | Note=C-type lectin;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00040 |
Q9BYZ8 | 55 | 101 | 51 | 59 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 51 | 59 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 73 | 83 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 73 | 83 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2KV3 |
Q9BYZ8 | 55 | 101 | 98 | 103 | Region | Note=Carbohydrate-binding |
Q9BYZ8 | 55 | 101 | 98 | 103 | Region | Note=Carbohydrate-binding |
Top |
SNVs in the skipped exons for REG4 |
- 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 |
UCEC | TCGA-AP-A05H-01 | exon_skip_29745 | 120341120 | 120341225 | 120341123 | 120341124 | Frame_Shift_Ins | - | A | p.N135fs |
LUSC | TCGA-85-6561-01 | exon_skip_29747 exon_skip_29748 | 120342348 | 120342485 | 120342482 | 120342482 | Nonsense_Mutation | C | A | p.E57* |
STAD | TCGA-CG-5721-01 | exon_skip_29745 | 120341120 | 120341225 | 120341118 | 120341118 | Splice_Site | A | G | p.N137_splice |
- 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 |
639V_URINARY_TRACT | 120342348 | 120342485 | 120342380 | 120342380 | Missense_Mutation | G | A | p.P91S |
SNU407_LARGE_INTESTINE | 120351326 | 120351486 | 120351373 | 120351373 | Missense_Mutation | C | T | p.R7Q |
NCIH513_PLEURA | 120351326 | 120351486 | 120351385 | 120351385 | Missense_Mutation | G | A | p.S3F |
LOXIMVI_SKIN | 120342348 | 120342485 | 120342372 | 120342372 | Nonsense_Mutation | C | T | p.W93* |
NCIH2373_PLEURA | 120341120 | 120341225 | 120341121 | 120341121 | Splice_Site | G | A | p.N136N |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for REG4 |
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 REG4 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for REG4 |
Top |
RelatedDrugs for REG4 |
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 REG4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |
REG4 | C0038356 | Stomach Neoplasms | 1 | CTD_human |