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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:RPLP2-CALR (FusionGDB2 ID:76681) |
Fusion Gene Summary for RPLP2-CALR |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RPLP2-CALR | Fusion gene ID: 76681 | Hgene | Tgene | Gene symbol | RPLP2 | CALR | Gene ID | 6181 | 811 |
| Gene name | ribosomal protein lateral stalk subunit P2 | calreticulin | |
| Synonyms | D11S2243E|LP2|P2|RPP2 | CRT|HEL-S-99n|RO|SSA|cC1qR | |
| Cytomap | 11p15.5 | 19p13.13 | |
| Type of gene | protein-coding | protein-coding | |
| Description | 60S acidic ribosomal protein P2acidic ribosomal phosphoprotein P2large ribosomal subunit protein P2renal carcinoma antigen NY-REN-44ribosomal protein, large, P2 | calreticulinCRP55ERp60HACBPSicca syndrome antigen A (autoantigen Ro; calreticulin)calregulinendoplasmic reticulum resident protein 60epididymis secretory sperm binding protein Li 99ngrp60 | |
| Modification date | 20200313 | 20200329 | |
| UniProtAcc | . | Q96L12 | |
| Ensembl transtripts involved in fusion gene | ENST00000321153, ENST00000532004, ENST00000530797, | ENST00000316448, | |
| Fusion gene scores | * DoF score | 25 X 15 X 6=2250 | 24 X 30 X 7=5040 |
| # samples | 26 | 38 | |
| ** MAII score | log2(26/2250*10)=-3.11334147307594 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(38/5040*10)=-3.72935241005633 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: RPLP2 [Title/Abstract] AND CALR [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | RPLP2(810303)-CALR(13054597), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Tgene | CALR | GO:0000122 | negative regulation of transcription by RNA polymerase II | 8107809 |
| Tgene | CALR | GO:0006611 | protein export from nucleus | 11149926 |
| Tgene | CALR | GO:0017148 | negative regulation of translation | 14726956 |
| Tgene | CALR | GO:0033144 | negative regulation of intracellular steroid hormone receptor signaling pathway | 8107809 |
| Tgene | CALR | GO:0034504 | protein localization to nucleus | 15998798 |
| Tgene | CALR | GO:0045665 | negative regulation of neuron differentiation | 8107809 |
| Tgene | CALR | GO:0045892 | negative regulation of transcription, DNA-templated | 8107809 |
| Tgene | CALR | GO:0048387 | negative regulation of retinoic acid receptor signaling pathway | 8107809 |
| Fusion gene breakpoints across RPLP2 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across CALR (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS5.0 | N/A | CA425105 | RPLP2 | chr11 | 810303 | - | CALR | chr19 | 13054597 | - |
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Fusion Gene ORF analysis for RPLP2-CALR |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| In-frame | ENST00000321153 | ENST00000316448 | RPLP2 | chr11 | 810303 | - | CALR | chr19 | 13054597 | - |
| intron-3CDS | ENST00000532004 | ENST00000316448 | RPLP2 | chr11 | 810303 | - | CALR | chr19 | 13054597 | - |
| In-frame | ENST00000530797 | ENST00000316448 | RPLP2 | chr11 | 810303 | - | CALR | chr19 | 13054597 | - |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000321153 | RPLP2 | chr11 | 810303 | - | ENST00000316448 | CALR | chr19 | 13054597 | - | 1153 | 447 | 563 | 15 | 182 |
| ENST00000530797 | RPLP2 | chr11 | 810303 | - | ENST00000316448 | CALR | chr19 | 13054597 | - | 760 | 54 | 435 | 758 | 108 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000321153 | ENST00000316448 | RPLP2 | chr11 | 810303 | - | CALR | chr19 | 13054597 | - | 0.46725893 | 0.53274107 |
| ENST00000530797 | ENST00000316448 | RPLP2 | chr11 | 810303 | - | CALR | chr19 | 13054597 | - | 0.7967306 | 0.20326947 |
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Fusion Genomic Features for RPLP2-CALR |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for RPLP2-CALR |
| Go to FGviewer for the breakpoints of chr11:810303-chr19:13054597 - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | CALR |
| FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. | FUNCTION: During spermatogenesis, may act as a lectin-independent chaperone for specific client proteins such as ADAM3. Required for sperm fertility (By similarity). CALR3 capacity for calcium-binding may be absent or much lower than that of CALR. {ECO:0000250, ECO:0000269|PubMed:21590275}. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 351_408 | 0 | 418.0 | Compositional bias | Note=Asp/Glu/Lys-rich | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 414_417 | 0 | 418.0 | Motif | Note=Prevents secretion from ER | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 18_197 | 0 | 418.0 | Region | Note=N-domain | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 191_255 | 0 | 418.0 | Region | Note=4 X approximate repeats | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 198_308 | 0 | 418.0 | Region | Note=P-domain | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 259_297 | 0 | 418.0 | Region | Note=3 X approximate repeats | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 309_417 | 0 | 418.0 | Region | Note=C-domain | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 191_202 | 0 | 418.0 | Repeat | Note=1-1 | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 210_221 | 0 | 418.0 | Repeat | Note=1-2 | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 227_238 | 0 | 418.0 | Repeat | Note=1-3 | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 244_255 | 0 | 418.0 | Repeat | Note=1-4 | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 259_269 | 0 | 418.0 | Repeat | Note=2-1 | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 273_283 | 0 | 418.0 | Repeat | Note=2-2 | |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 287_297 | 0 | 418.0 | Repeat | Note=2-3 |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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Fusion Gene Sequence for RPLP2-CALR |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >In-frame_ENST00000321153_ENST00000316448_CA425105_RPLP2_chr11_810303_-_CALR_chr19_13054597_length(transcript)=1153nt_BP=447nt GGCATGCTGGGGGTGCTAGGTACCGAAGGCAGATGCCGTCCCTTTGGACTCGCTTCGTCCAACGCCCCCACGAGTTTCGGTGGCCCTTCG CCCCACGCTATAAGAGCAGTCACTTCCGGAACTGCTGCCCTTCGCCTTTGCCGCGAAAAGTGCCTGACGGGGGCTGGGAAGGGGGAGGGG GAAGGAGTCAACGACTCCCTCCCCGTCGTCATTGGCTGAGCGCCTCGTGACGTCACTCTGAGGCGCCTCATGCGGCGCCGCGCACGGGTC CCAGAGCCTTCTGGGTAGCGGTTTAACCCCGCCTCTTGCGTCGGCGCCTTCCTTTTCCTCCCTGTCGCCACCGAGGTCGCACGCGTGAGA CTTCTCCGCCGCCTCCGCCGCAGACGCCGCCGCAAGAAGATCTTGGACAGCGTGGGTATCGAGGCGGACGACGACCGGCTCAACAAGACG CAAAGAGGAGGAGGAGGCAGAGGACAAGGAGGATGATGAGGACAAAGATGAGGATGAGGAGGATGAGGAGGACAAGGAGGAAGATGAGGA GGAAGATGTCCCCGGCCAGGCCAAGGACGAGCTGTAGAGAGGCCTGCCTCCAGGGCTGGACTGAGGCCTGAGCGCTCCTGCCGCAGAGCT GGCCGCGCCAAATAATGTCTCTGTGAGACTCGAGAACTTTCATTTTTTTCCAGGCTGGTTCGGATTTGGGGTGGATTTTGGTTTTGTTCC CCTCCTCCACTCTCCCCCACCCCCTCCCCGCCCTTTTTTTTTTTTTTTTTTAAACTGGTATTTTATCTTTGATTCTCCTTCAGCCCTCAC CCCTGGTTCTCATCTTTCTTGATCAACATCTTTTCTTGCCTCTGTCCCCTTCTCTCATCTCTTAGCTCCCCTCCAACCTGGGGGGCAGTG GTGTGGAGAAGCCACAGGCCTGAGATTTCATCTGCTCTCCTTCCTGGAGCCCAGAGGAGGGCAGCAGAAGGGGGTGGTGTCTCCAACCCC CCAGCACTGAGGAAGAACGGGGCTCTTCTCATTTCACCCCTCCCTTTCTCCCCTGCCCCCAGGACTGGGCCACTTCTGGGTGGGGCAGTG >In-frame_ENST00000321153_ENST00000316448_CA425105_RPLP2_chr11_810303_-_CALR_chr19_13054597_length(amino acids)=182AA_start in transcript=563_stop in transcript=15 MAWPGTSSSSSSSLSSSSSSSSSLSSSSSLSSASSSSLRLVEPVVVRLDTHAVQDLLAAASAAEAAEKSHACDLGGDREEKEGADARGGV KPLPRRLWDPCAAPHEAPQSDVTRRSANDDGEGVVDSFPLPLPSPRQALFAAKAKGSSSGSDCSYSVGRRATETRGGVGRSESKGTASAF -------------------------------------------------------------- >In-frame_ENST00000530797_ENST00000316448_CA425105_RPLP2_chr11_810303_-_CALR_chr19_13054597_length(transcript)=760nt_BP=54nt AAGAAGATCTTGGACAGCGTGGGTATCGAGGCGGACGACGACCGGCTCAACAAGACGCAAAGAGGAGGAGGAGGCAGAGGACAAGGAGGA TGATGAGGACAAAGATGAGGATGAGGAGGATGAGGAGGACAAGGAGGAAGATGAGGAGGAAGATGTCCCCGGCCAGGCCAAGGACGAGCT GTAGAGAGGCCTGCCTCCAGGGCTGGACTGAGGCCTGAGCGCTCCTGCCGCAGAGCTGGCCGCGCCAAATAATGTCTCTGTGAGACTCGA GAACTTTCATTTTTTTCCAGGCTGGTTCGGATTTGGGGTGGATTTTGGTTTTGTTCCCCTCCTCCACTCTCCCCCACCCCCTCCCCGCCC TTTTTTTTTTTTTTTTTTAAACTGGTATTTTATCTTTGATTCTCCTTCAGCCCTCACCCCTGGTTCTCATCTTTCTTGATCAACATCTTT TCTTGCCTCTGTCCCCTTCTCTCATCTCTTAGCTCCCCTCCAACCTGGGGGGCAGTGGTGTGGAGAAGCCACAGGCCTGAGATTTCATCT GCTCTCCTTCCTGGAGCCCAGAGGAGGGCAGCAGAAGGGGGTGGTGTCTCCAACCCCCCAGCACTGAGGAAGAACGGGGCTCTTCTCATT TCACCCCTCCCTTTCTCCCCTGCCCCCAGGACTGGGCCACTTCTGGGTGGGGCAGTGGGTCCCAGATTGGCTCACACTGAGAATGTAAGA >In-frame_ENST00000530797_ENST00000316448_CA425105_RPLP2_chr11_810303_-_CALR_chr19_13054597_length(amino acids)=108AA_start in transcript=435_stop in transcript=758 MINIFSCLCPLLSSLSSPPTWGAVVWRSHRPEISSALLPGAQRRAAEGGGVSNPPALRKNGALLISPLPFSPAPRTGPLLGGAVGPRLAH -------------------------------------------------------------- |
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Fusion Gene PPI Analysis for RPLP2-CALR |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| Tgene | CALR | chr11:810303 | chr19:13054597 | ENST00000316448 | 0 | 9 | 237_270 | 0 | 418.0 | PPIB |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs for RPLP2-CALR |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Tgene | CALR | Q96L12 | DB11348 | Calcium Phosphate | Ligand | Small molecule | Approved |
| Tgene | CALR | Q96L12 | DB11348 | Calcium Phosphate | Ligand | Small molecule | Approved |
| Tgene | CALR | Q96L12 | DB14481 | Calcium phosphate dihydrate | Small molecule | Approved | |
| Tgene | CALR | Q96L12 | DB14481 | Calcium phosphate dihydrate | Small molecule | Approved | |
| Tgene | CALR | Q96L12 | DB11093 | Calcium citrate | Ligand | Small molecule | Approved|Investigational |
| Tgene | CALR | Q96L12 | DB11093 | Calcium citrate | Ligand | Small molecule | Approved|Investigational |
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Related Diseases for RPLP2-CALR |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | RPLP2 | C0006142 | Malignant neoplasm of breast | 1 | CTD_human |
| Hgene | RPLP2 | C0678222 | Breast Carcinoma | 1 | CTD_human |
| Hgene | RPLP2 | C1257931 | Mammary Neoplasms, Human | 1 | CTD_human |
| Hgene | RPLP2 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
| Hgene | RPLP2 | C4704874 | Mammary Carcinoma, Human | 1 | CTD_human |
| Tgene | CALR | C0001815 | Primary Myelofibrosis | 2 | CTD_human;GENOMICS_ENGLAND;ORPHANET |
| Tgene | CALR | C0026987 | Myelofibrosis | 2 | GENOMICS_ENGLAND;ORPHANET |
| Tgene | CALR | C0033975 | Psychotic Disorders | 2 | PSYGENET |
| Tgene | CALR | C0036337 | Schizoaffective Disorder | 2 | PSYGENET |
| Tgene | CALR | C0040028 | Thrombocythemia, Essential | 2 | CTD_human;ORPHANET |
| Tgene | CALR | C0349204 | Nonorganic psychosis | 2 | PSYGENET |
| Tgene | CALR | C0004565 | Melanoma, B16 | 1 | CTD_human |
| Tgene | CALR | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| Tgene | CALR | C0009075 | Melanoma, Cloudman S91 | 1 | CTD_human |
| Tgene | CALR | C0009402 | Colorectal Carcinoma | 1 | CTD_human |
| Tgene | CALR | C0009404 | Colorectal Neoplasms | 1 | CTD_human |
| Tgene | CALR | C0018598 | Melanoma, Harding-Passey | 1 | CTD_human |
| Tgene | CALR | C0025205 | Melanoma, Experimental | 1 | CTD_human |
| Tgene | CALR | C0027022 | Myeloproliferative disease | 1 | CTD_human |
| Tgene | CALR | C0027626 | Neoplasm Invasiveness | 1 | CTD_human |
| Tgene | CALR | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| Tgene | CALR | C0033937 | Psychoses, Drug | 1 | PSYGENET |
| Tgene | CALR | C0036349 | Paranoid Schizophrenia | 1 | PSYGENET |
| Tgene | CALR | C0036939 | Shared Paranoid Disorder | 1 | PSYGENET |
| Tgene | CALR | C0151744 | Myocardial Ischemia | 1 | CTD_human |
| Tgene | CALR | C0279626 | Squamous cell carcinoma of esophagus | 1 | CTD_human |
| Tgene | CALR | C0376358 | Malignant neoplasm of prostate | 1 | CTD_human |
| Tgene | CALR | C3277671 | THROMBOCYTHEMIA 1 | 1 | GENOMICS_ENGLAND |
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