Gene Fusions Tutorial
Data Exploration
In the following section we will use the ucsc genome browser’s online blat to explore a number of example positive and negative fusion transcripts.
Understanding strand and breakpoint position
HCC1395 RNA-Seq
Example 1: PLA2R1-RBMS1
The following two sequence predicted by defuse represent two distinct splice variants of the PLA2R1-RBMS1 fusion.
>771050
AAGATGCAAGAAACTGTGCTGTTTATAAGGCAAACAAAACATTGCTGCCCTTACACTG
TGGTTCCAAACGTGAATGGATATGCAAAATCCCAAGAGATGTGAAACCCAAGATTCCG
TTCTGGTACCAGTACGATGTACCCTGGCTCTTTTATCAGGATGCAGAATACCTTTTTC
ATACCTTTGCCTCAGAATGGTTGAACTTTGAGTTTGTCTGTAGCTGGCTGCACAGTGA
TCTTCTCACAATTCATTCTGCACATGAGCAAGAATTCATCCACAGCAAAATAAAAGCG
|CAACAGGAACAAGATCCTACCAACCTCTACATTTCTAATTTGCCACTCTCCATGGAT
GAGCAAGAACTAGAAAATATGCTCAAACCATTTGGACAAGTTATTTCTACAAGGATAC
TACGTGATTCCAGTGGTACAAGTCGTGGTGTTGGCTTTGCTAGGATGGAATCAACAGA
AAAATGTGAAGCTGTTATTGGTCATTTTAATGGAAAATTTATTAAGACACCACCAGGA
GTTTCTGCCCCCACAGA
>770399
GGATTGGATTTAATAAAAGAAACCCACTGAATGCCGGCTCATGGGAGTGGTCTGATAG
AACTCCTGTTGTCTCTTCGTTTTTAGACAACACTTATTTTGGAGAAGATGCAAGAAAC
TGTGCTGTTTATAAGGCAAACAAAACATTGCTGCCCTTACACTGTGGTTCCAAACGTG
AATGGATATGCAAAATCCCAAGAGATGTGAAACCCAAGATTCCGTTCTGGTACCAGTA
CGATGTACCCTGGCTCTTTTATCAGGATGCAGAATACCTTTTTCATACCTTTGCCTCA
GAATGGTTGAACTTTGAGTTTGTCTGTAGCTGGCTGCACAGTGATCTTCTCACAATTC
ATTCTGCACATGAGCAAGAATTCATCCACAGCAAAATAAAAGC|GCAACAGGAACAAG
ATCCTACCAACCTCTACATTTCTAATTTGCCACTCTCCATGGATGAGCAAGAACTAGA
AAATATGCTCAAACCATTTGGACAAGTTATTTCTACAAGGATACTACGTGATTCCAGT
GGTACAAGTCGTGGTGTTGGCTTTGCTAGATTTTTTTTTTTTTTTGTGAGAAATA
Web-blatting them will give you the following list of alignments.
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN
---------------------------------------------------------------------------------------------------
browser details 770399 389 1 392 576 100.0% 2 - 160832579 160836405 3827
browser details 770399 184 392 576 576 100.0% 2 - 161159310 161159999 690
browser details 770399 155 392 550 576 98.8% 12 - 66628514 66628672 159
browser details 770399 78 392 547 576 75.0% 12 - 94818206 94818361 156
browser details 770399 27 361 391 576 96.6% 2 - 5782745 5783131 387
browser details 770399 22 104 125 576 100.0% 5 + 148444986 148445007 22
browser details 770399 21 438 458 576 100.0% 6 - 158134531 158134551 21
browser details 770399 20 265 284 576 100.0% 5 - 84000186 84000205 20
browser details 770399 20 235 266 576 81.3% 2 + 74143821 74143852 32
browser details 771050 288 1 290 538 100.0% 2 - 160832579 160833890 1312
browser details 771050 241 290 538 538 98.4% 12 - 66628424 66628672 249
browser details 771050 238 290 528 538 100.0% 2 - 161157162 161159999 2838
browser details 771050 83 290 453 538 75.5% 12 + 56965481 56965649 169
browser details 771050 39 462 520 538 83.1% 3 + 29804414 29804472 59
browser details 771050 27 259 289 538 96.6% 2 - 5782745 5783131 387
browser details 771050 27 441 472 538 96.7% 3 + 192743568 192743603 36
browser details 771050 25 461 493 538 76.7% 2 - 182283137 182283166 30
browser details 771050 22 2 23 538 100.0% 5 + 148444986 148445007 22
browser details 771050 21 336 356 538 100.0% 6 - 158134531 158134551 21
browser details 771050 20 163 182 538 100.0% 5 - 84000186 84000205 20
browser details 771050 20 1 24 538 91.7% 1 + 162028403 162028426 24
Click ‘browser’ for the first alignment for the alignment to the PLA2R1 gene.
Do you expect the genomic breakpoint to be upstream (on the left) or downstream (on the right) relative to the aligned sequences?
> upstream (on the left)
Go back and click ‘browser’ for the second alignment for the alignment to the RBMS1 gene.
Do you expect the genomic breakpoint to be upstream (on the left) or downstream (on the right) relative to the aligned sequences?
> downstream (on the right)
The following sequence is a destruct breakpoint prediction most likely associated with the fusion.
>destruct_31240
TGCAAAAGATCTGGAAAAATGCAGTCTGGTATTTACACATAATTTAAGTTCACAGTGC
AACTGCTCCCATAACCCTAGCTGAAACTGTCTCTTCTTAGTCATTTTTAATTTTCCAA
GATAACTTGGCAAAGCTATTGTTGTTGACATAATAAAGACTGGGCAGAAGGCTTACCT
AGCAAAGCCAACACCACGACTTGTACCACTGGAATCACGTAGTATCCTTGTAGAAATA
ACTTGTCCAAATGGTTTGAGCATATTTTCTAGTTCTTGCTCATCCATGGAGAGTGGCA
AATTAGAAATGTAGAGGTTGGTAGGATCTTGTTCCTGTTGCTAAAACAGAAGAGAGTG
TTGTCCATTAATTTCCAACAGAAGGTGAGATATTTATGTTAACACACCTATTTTTATT
AGCTACTTTCTTTGCTCAAGTCCTTTTAAAGTACTCAGAACCTCAGAACACCAAAGTC
ACCCTGGACTCTTGAAAATAGTGTCTGAAGCTTGGACAA[AA]AAAAAGTAATATTAG
AAAATGAATTCATTTTCTGACAAAAAATTATTGGCTCATCCTCTCAGTTATTTACCCT
CTCAGTGATTTATAATTCATTGCATATGTCACATGTATTTGAAAAACAATTCAAGGTA
TCAAGGCATCATTAGTATAAAGATACTGATTTTAGGTATTAGTCTGATTGCTAAGCTT
TAAGCAGTATAAGCTTTCCTTCCCATTCAAATAGAGAGACACAATATAGGACAAAAGA
ATACTACAGAGTGCCCAGTGTTTGACAACTAGAAAATTATCCTTTTGATGAGTTCATG
TCCTTTGCAGGGACATGGATGAAGCTGGAAACCATCAATCTCAGCAAACTAACACATG
AACAGAAAACCAAACACCGCATGTTCTCACTCATAAGTGGGAGCTGAACAATGAGAAC
ACATGGACACAGGGAGGGGAACATCACACACTGGGGCCTGTCGG
Add the breakpoint sequence to the web blat query, click on the same alignments as above, and zoom out to see the position of the breakpoint relative to the fusion.
To view the alignments supporting the fusion in IGV, click File->Open URL and copy/paste the following URL into the text box for PLA2R1:
http://cbwmain.dyndns.info/Module7/bams/genes/HCC1395_PLA2R1.bam
Then zoom to chr2:160,832,138-160,833,113.
You can also add the following URL for RBMS1.
http://cbwmain.dyndns.info/Module7/bams/genes/HCC1395_RBMS1.bam
Then zoom to chr2:161,159,715-161,160,281.
Example 2: RAB7A-LRCH3
Web blat the following three predictions involving LRCH3.
>2827083
CTCCGAGATCACAAGGTAGAGACACTTTCAACCGGTACTCAATATGTTTACGCAGTTG
GTCTATTAATTCCAGCTCTTCTTCTCTCTGTCTTGAATTCTGTCCTGTTATGGAATCT
GTAGAATCAGTGGTAGGTGCAGCAGATGGAGGAAGGGGTGAAGCATGACCTGTTTCTG
TTGCAGGTGAACTTAATAGAGCATTAGGTCTGTCATCACTC|GCGGCCGCTGCGCTGG
GGGCTCCGGGCCGGGCGCGTCGCGAGGGCTCCCGCCGAGGAGGAGACTAAACGGAGGA
CAGAAGCGAGAAGGTCCAAGTTCTGGTTCCAGGGAACTCTCCCGAGCTCTCCAAGCCG
CCAACTCCGCCGCTGCCGCCGCCTCAGGCTTTATGGCCAAGACTCCAGGCCCGCTCCC
ACTTCCGCCACCGCCG
>2831138
GGAGCAGCTCTAACTGACGGTGTTGTTCTTTGCCATTTGGCCAATCATGTGCGACCTC
GATCTGTCCCAAGCATTCATGTTCCCTCACCAGCTGTACCTAAATTAACAATGGCGAA
ATGCAGGCGAAATGTGGAAAATTTCCTAGAAGCTTGCAGAAAAATTGGTGTACCTCAG
|AGCATAAAAAGATGGAAAGCTTCCAATTCACGCTGCCAAGCATAACTCTGACAGCAA
TTCAACAAAGCAGCACCAAAAAATACACCTACAGGTTAATCTCACTTGTGGAATATAT
AAACACAAAGTAAAAGTCTAGGCTGGCTGTGGCGGCAGGTACCTAGAATCCCAGCTCC
TTGGAGGCTGAGGTGGGAGGATTGCTTGAGCCCAGGAGTTTAAGACCAGCCTGGGCAA
CACAGTGAGAACCCCTGTCTCA
>2831232
GAGCGGGCCTGGAGTCTTGGCCATAAAGCCTGAGGCGGCGGCAGCGGCGGAGTTGGCG
GCTTGGAGAGCTCGGGAGAGTTCCCTGGAACCAGAACTTGGACCTTCTCGCTTCTGTC
CTCCGTTTAGTCTCCTCCTCGGCGGGAGCCCTCGCGACGCGCCCGGCCCGGAGCCCCC
AGCGCAGCGGCCGCG|AGTGATGACAGACCTAATGCTCTATTAAGTTCACCTGCAACA
GAAACAGTTCATCATTCCCCTGCATATTCTTTTCCTGCTGCTATCCAGAGAAATCAGC
CTCAGCGCCCTGAAAGCTTCCTTTTCCGAGCAGGTGTCAGGGCAGAAACCAACAAAGG
TCATGCTTCACCCCTTCCTCCATCTGCTGCACCTACCACTGATTCTACAGATTCCATA
ACAGGACAGAATTCAAGACAGAGAGAAGAAGAGCTGGAATTAATAGACCAACTGCGTA
AACATATTGAGTAC
For each prediction, is the breakpoint upstream or downstream?
> 2831232: upstream (to the left)
> 2827083: upstream (to the left)
> 2831138: downstream (to the right)
Is it possible that all three fusion transcripts arrised from the same breakpoint?
> No
Web blat the RAB7A-LRCH3 breakpoint.
>58737
TCGCATTTTCTGGTATTTTGTATAAATGGGATCTGTATATATACTTTAAGTATACTGT
GTATTTATTTGGGGGGGAGTATCTGGCCTCATTCGACATTATTATTTTATTTGTGCTG
TATGTATCTATAGTTCATTCCTTTTTGTAGCTCAGTGGTATTTCATTGTATAGCTATA
TCACAGTTTGATTAGCCTTTCTGTTGATGGACATTTGGGTTGATTCACGTTTCTGGCT
GTTACAACAAAAGCTGCTGTGAACACTGGTGCACAAGTCTCTGTCTAGATCTGTGTTT
TCATTTCCTTTGGGTAGGTAGCTGTTTCGGAGGGGAATGGTTGGGGCATATGGTAGGC
ATATGCTTTAACTTTGTTTAAAAAGTTGAAATACTTAATACATCATAAAATTTGCCTA
TGTAAAGTGTGCGTGTTTTGTTTTGTTTTGTTTTGTTTTTGGAGACAGGGTCTCATTC
TGTTGCGCAGGCTGGAGTGTAATAGTTTGATCACAGCT[]CAGGAGAATCACTTGAAC
CCGAAAGGCAGAGGTTGTGGTGAGCTGAGAGTGCTCTATTGCACTCTAGCCTGGGCAA
CAAGAGCGAGACTCCATCTCAAAAATAAAAAATAAAAACAGCTGGGCGTGGTGGCTCA
TGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGAATCACCTGAGGTTGGGAG
TTCGAGAACGGCCTGACTAACATGGAGAAACCCCGTATCTACTAAAAATACAAAAAAA
TTAGCTGGGTATGGTGGTGCATGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGG
AGAATTGCTTGAACCCGGGAGGCGGAGGTTGTGGTGAGCTGAGATCGTGCCATTGCAC
TCCAGCCTGGGCAATAAGAGCTAAACTCCATCTCAAAAAAAAAAAAACAAAAAACAAA
AAAACAAAAACTTGGCTTTTAAAAATACAGAATTAATTCATTTCACCAAATCCTCATT
TCTTTTTCTTCTTCTTCTTTTTTTTTTTTTTTT
Which transcripts does this breakpoint explain?
> 2831232, 2827083
Identifying false positives
313B RNA-Seq
Example 1
>19455
CAGGAAATCTTCAGCAAGCTGTCTTACTTCTTTTGGCCAAGTCGCACTCCACATTAGA
GTTTGCCTATCAGGTCTTATTTGATCCACAATCTTCCTTATTTGGGGT|TCAAATCCC
ATATCCAGCATCCTATCAGCTTCATCCAACACTAAGTACTTGCAGAAGTCTAATCC
Notice that in the alignment summary, the best matches overlap in the query sequence. In deFuse this prediction is given a lower probability according to the breakpoint homology feature.
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN
---------------------------------------------------------------------------------------------------
browser details 19455 132 1 141 171 97.2% 17 + 62499145 62499374 230
browser details 19455 96 2 154 171 88.8% 22 + 38890737 38890976 240
browser details 19455 67 104 171 171 100.0% Y - 15027123 15027592 470
browser details 19455 62 108 171 171 98.5% X - 73350813 73350876 64
browser details 19455 40 88 141 171 87.1% 6 - 74118977 74119030 54
browser details 19455 32 84 116 171 100.0% 22 - 49607171 49613016 5846
browser details 19455 22 92 114 171 100.0% 4 + 72709432 72709456 25
browser details 19455 21 95 116 171 100.0% 6 + 131014581 131014603 23
browser details 19455 20 93 112 171 100.0% 2 - 157047083 157047102 20
browser details 19455 20 101 122 171 95.5% 14 - 29461851 29461872 22
browser details 19455 20 1 20 171 100.0% 3 + 175393751 175393770 20
Example 2
>29877
CTGTTTCCTCTTTTACCAAGGACCCGCCAACATGGGCCG|GCTATCTTGTTGCGGAGCTT
CTTGCTGGGGATAATGGCGATCTCCTTGCACACGCGCTTGTTCGTGTG
Blat the sequence. Notice in the alignment summary, one part of the query sequence maps to many locations in the genome. Although one of the alignments may represent a true fusion, the prediction is more likely a mapping artifact.
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq 68 40 107 107 100.0% 22 - 32435560 32435627 68
browser details YourSeq 64 40 107 107 97.1% 15 + 82824392 82824459 68
browser details YourSeq 64 40 107 107 97.1% 15 + 83208735 83208802 68
browser details YourSeq 62 40 107 107 95.6% 5 - 116052023 116052090 68
browser details YourSeq 60 40 107 107 94.2% 17 - 29158008 29158075 68
browser details YourSeq 58 40 107 107 92.7% 1 + 167131923 167131990 68
browser details YourSeq 57 44 102 107 98.4% 6 - 63257401 63257459 59
browser details YourSeq 54 44 107 107 92.2% 6 + 50825228 50825291 64
browser details YourSeq 54 41 106 107 85.8% 3 + 143574838 143574900 63
browser details YourSeq 37 44 88 107 91.2% 7 - 37156486 37156530 45
browser details YourSeq 35 1 35 107 100.0% 15 - 82824833 82824867 35
browser details YourSeq 35 1 35 107 100.0% 15 - 83209176 83209210 35
browser details YourSeq 34 40 75 107 97.3% 11 + 110976470 110976505 36
browser details YourSeq 30 8 39 107 96.9% 22 + 32435452 32435483 32
browser details YourSeq 20 1 20 107 100.0% 5 + 144765194 144765213 20
Example 3
>40571
TAGAATTAGAATTGTGAAGATGATAAGTGTAGAGGGAAGGTTAATAGTTGATATTGCTAG
TGTGGCGCTTCCAATTAGGTGCATGAGTAGGTGGCCTGCAGTAAT|GTTAGCGACAGGGA
GGGATGCGCGCCTGGGTGTAGTTGTGGGGGAGGAAGTGGCTAGCTCAGGGCTTCAGGGGA
CAGACAGGGAGAGATGACTGAG
Blat the sequence and select the first alignment result. Ensure you have the NUMT track turned on in UCSC. This fusion prediction is actually a NUMT insertion in the patient’s genome.
Example 4
>33864
CCAGGGCGCCATTGAGCGGCGAGGGGGTGAGGGGGTTGACGGTGGCGGTGGTCCTGGTCG
CGGTGGAAAGCATCCCTAGCGAAGGGGACTTGGGCTCATGGCTCATGCCTG|CACCAGTA
AGGTCTGGTCCGTCCTCCTCCCGGCTGCTCTGCAGACACTGTGCTGGCCTCAGCTCCTGG
GCCATCCTGGGGCCTCTGGGCAG
>17735
CATGGGCACGCGCTTGGGTGTGCTGGCGGGGGAGCTGTGGTTGGTGGCCGGAGAGGACAC
GGGGGACGACTCGCTGCTCAGTGAGGACC|CTGCACCAGTAAGGTCTGGTCCGTCCTCCT
CCCGGCTGCTCTGCAGACACTGTGCTGGCCTCAGCTCCTGGGCCATCCTGGGGCCTCTGG
GCAGGGTCTCCGTGGGGGCGCGTGGCCGGGTCTCGGACT
Blat both sequences and select the first alignment results. These are examples of likely read through chimeras.
Example 5
>5655
TGATCAAGCAACTTCCCTGAGGATCCTCAACAATGGTCATGCTTTCAACGTGGAGTTTGA
TGACTCTCAGGACAAAGC|AGAACGTAAGCTCCATGAGGACCAGGAAGTCTGTCTGCTTT
GTTCACTGCTGGATCCCGTGACTCGGAACAGTGCACGTAACAGGTGTTCAATAAACCTTT
GTTGAATGAATAAGTGAA
>11908
TCTGTTTCCTATGATCAAGCAACTTCCCTGAGGATCCTCAACAATGGTCATGCTTTCAAC
GTGGAGTTTGATGACTCTCAGGACAAAGC|AGGGGCTCTTTCCAGGATTCCTGGGTGATG
GTGCATGATTCTAACAAGCAACAACAGAGGATGAACCCCCGGCCAGATTCAGAAAACCCC
ACGCCCCTTCCAGGCA
Blat both sequences. Select browser for any alignment result and then browse to chr1:110,721,056-110,731,655 and chr8:86,373,054-86,382,253. This is an example of rearrangement inducing spurious intronic transcription.
Example 6
>37434
TTGGCATCAAATAGATGAACAGGAGAAAAGCTGTTTTAATGTATGTACTCACAGATGGGA
ATCCCACAAGAATATGAGACTTAAAGAACAGGCCAGGT|TATTCCAGGATCTTTGGAGAC
CCGAGGAAAGCCGTGTTGACCAAAAGCAAGACAAATGACTCACAGAGAAAAAAGATGGCA
GAACCAAGG
>26643
CCGGGACAGTCTGAATCATGTCCTTCAGTAAGCCAGCCCATCTACCAGCTGTTCAGAACC
TGACGGCTTTAGTTGCCCTTGGTTCTGCCATCTTTTTTCTCTGTGAGTCATTTGTCTTGC
TTTTGGTCAACACGGCTTTCCTCGGGTCTCCAAAGATCCTGGAATAACCT|TCCTGGTGG
AGTAGAAGTAGTCTATAGCTTCTCCTTGGTAGTCCAGATGGGTCTCCCCAGCCAATGCAT
AACTCTCTCTTTGCCTTTTGATTCAGAGGCATGTGGAGCTCAGCGTGGCCAGGT
>29118
AGTAAGCCAGCCCATCTACCAGCTGTTCAGAACCT|AGAGGTCTTAGTTCCGGAGGGAGG
AATGCTGCCACCAGGAGACACAACAATGATTCAATTAAACTAGAATTTACGACTGC
>29539
AGGCACACTCAAACAACGACTGGTCCTCACTCACAACTGATAAGGCTTCCTTGATATGAG
CTGCTGGGTCCGGGACAGTCTGAATCATGTCCTTCAGTAAGCCAGCCCATCTACCAGCTG
TTCAGAACCTGACGGCTTTAGTTGCCCTTGGTTCTGCCATCTTTTTTCTCTGTGAGTCAT
TTGTCTTGCTTTTGGTCAACACGGCTTTCCTCGGGTCTC|CAAAGCCATCTTGCTGTTAT
CAACAGCATCGAGTAATGATAGGTATCTGGAATGTTCAATATGACCTGCCGCGCTCCAGG
CGGCGCTCCCCGCCCCTCGCCCTCCGCCTCCGCCTCCGCCTCCTGCTTAGCTCGCGCCTA
CTCG
>29538
TTCAGAACCTGACGGCTTTAGTTGCCCTTGGTTCTGCCATCTTTTTTCTCTGTGAGTCAT
TTGTCTTGCTTTTGGTCAACACGGCTTTCCTCGGGTCTCCAAAGATCCTGGAATA|ACCT
GTCCAGTAGTTCTGTAGCGGAGCAGGGCAGGTCCTACTTCTTCAAAAGCACTCAGTAAAG
GTGGGGAAGTCCTGAGCAACCT
>29535
AGGCTTCCTTGATATGAGCTGCTGGGTCCGGGACAGTCTGAATCATGTCCTTCAGTAAGC
CAGCCCATCTACCAGCTGTTCAGAACCTGACGGCTTTAGTTGCCCTTGGTTCTGCCATCT
TTTTTCTCTGTGAGTCATTTGTCTTGCTTTTGGTCAACACGGCTTTCCTCGGGTCTCCAA
AGATCCTGGAATA|ACCTGCCGCGCCGCGCTCCTCACACCCGCTTTCACCTCCGGGCGGG
GCAGGGGGCATCGGCGGGTCCCAGGCGCCCAGGTTCCCCTCCCCAGCCCGGACCCCGAGC
CGGGACCCTGGTACCGGCGCCGCTCACCTGCCGCGCTCCAGGCGGCGCTCCCCGCCCCTC
GCCCTCCGCCTCCGCCTCCGCCTCCTGCTTAGCTCGCGCCTACTCGGC
>37354
ACCCTCCAAAGCAACATGAAATGAAACCAAACCACAATAACAACCAAATGAAATAAGACT
GACAAGAAGTATGCGGTCATGGCCAATACATGGCT|CGATTTTTTTTTCTTTAACATGCA
CCTTCCTGAGCAAATAAAGGGCTTTTTTCCACCCCTTCCCGCTTGGCTTTAAATGACCAA
AGAATATT
>20051
TGGAATGTTCAATATGACCTGCCGCGCTCCAGGCGGCGCTCCCCGCCCCTCGCCCTCCGC
CTCCGCCTCCGCCTCCTGCTTAGCTCGCGCCTA|CTCCAGCGACTATGGACAGACTTCCA
AGATGAGCCCACGCGTCCCTCAGCAGGATTGGCTGTCTCAACCCCCAGCCAGGGTCACCA
TCAAAATGGAATGTAACCCTAGCCAGGTGAATGGCTCAAGGAACTCTCCTGATGAATGCA
GTGTG
Blat all the sequences and select browser for any alignment result. Then navigate to TMPRSS2 and ERG.
This is an example TMPRSS2-ERG fusion. Notice some predictions are spliced and there are many variants.
313B Complex breakpoints (optional)
Example 7
>fusion_27034
ACAGGGACGTCAGGCCACACAGGAGAAGCAGCGCGCCAATTACCACTAGCAACCATATATACCAGAGATGTACCCAGTCTGTGGTCAGGC
AA|CAACTCCACGGGAGGCAAGGCCTGACAGGCTGAAGTCACCTTTGCTTCACATTTTCTGTGCGTCGCCACCTTGCAGACTCTGCACGA
AACGCCTGTCCCATCGATGGTCACCTTA
>breakpoint_86623
TGGCTTTGGGTAAAAACATGCTGTCAGCAGTGTTATTTTGAGTGCTTAAGATGACAAAAACACGTCTTTATTTTGTGATAAGTCATCTAT
GAGATCTATTACTTAAGTAAAAATAAATAAAAAGAAGTCATAGATGTCTAATGACATCTTGACTCTCTTTTGGGNGTTGGGTGCCACCTA
CAGTGTGCAAATTTTCACTAAGAAAGGGAAGTTTTTCTTGCATTCACATCTCTATTGGAAGAAGGGAAAACAATAACACCACGAAAGCAC
CATAATCATTCCTATGCCAGCTTTCTACATTTGAGTTACCTTTCTTCAAAGTGGAAAGGTGGCTCATGCCTGTAATCCCAGCACTTTGGG
AGGCTGAGGCGGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCTCGACCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAG
>breakpoint_70139
TTGTGCCCTTGGGCCTGCTGGGGGTAGGACTCCTCTCCCCTTATCCAGTACAGCCTTCAAAAGGACACTGACATTCCCTTCCCCTGTCCC
CAAGGCCCACATTGGTCCTTGCCCCTGCTGTAACTAACCACTCCCTTTTCCTCCCCCATCTCCCTCTAGCGGCGAAACACGGCCCCAGTC
AGGCGCATAGAGCACCTGGTAAGGTGATGCTGGAGCAGGAGGGGGAAGCAGGTAGCTTTGGGAGTAAGGATCTAGATTTCCTGAAGACAA
AAAGGGCATGGCTCTGGAGTGGGCAGTCTAGAGTAGGGGGTACCCAAAGAGATGTCTAGACACTGTCTGTTAACCACCAGGGATCCACCA
AATCTCTGAACCACTCAAAGCAGCGCAGCACTCTNCATGAGCCCAGGGTTTTCCGGTTTCTGGCTCAGCTCCCAATCTCAAACACAAGGC
CTAGAGAAGCACTTAAGTCACCCATCTGACTTAGATAAATGCACCTTTGCAGAGACCCTCACTAAGCTCTGCCTCCCTGGTCTGTCTTGT
CCATCTGAGAAATGGGGATGCCCTGTCCCACTGGTTTTCAGATGATGGTCAGGGAGCCCCATGGGCTCCCCTGACATGCAAGGAGAAGAG
GATGTGTTTAGGGCTCAGTACTTCCCCAGGCCCCCAATAAACACACAATCTAATAACTGCTTGCTGTGTAAGCACAGCTTAAAGACGAGT
TCCTTAGCCTCCAAACTCTTGCTCCTGAAGGACCTTTTCAGCACTGACTTGGGAGGTATCCAAGTGTCAAAGCCAGGAGGACTTGGCTGC
AGCC
Blat the above sequences and visit the following genomic locations to view the path:
chr12:10,333,497-10,341,218
chr20:30,520,386-30,535,106
chr12:53,444,452-53,449,049
Trinity assembly of simulated reads (optional)
Example 8
>c0_g2_i1 len=2314 path=[553:0-550 1104:551-1144 3516:1145-1762 25:1763-2313]
TTCTCTTACATGTTGGACTTTATAGAATGAAATGCCAGAGATTTGATATTTATTATCTGA
AATAGGTTTAACATTTGGAGAAATGTGTTCAAACACACAACCTTGGAAAGAAAAGCAAGC
TGATAGGTCAGAGAACAGAGGGTGGGCAGAAAACACGATGTGCATAATTTTGCTGCGTGT
TGGGCAAAAAGTTAGAAAACTGGGTTCTTTGGAGAATAAAGAGCTCTCAGATGAGGTAAA
GGTAAAACACAAATAAATTTCCAACCCTTGATGAGGGCCACGAGATATCAATTTTAAATA
TATATGACCACAATATCAATAATGAAGAAATCTTACGTTTTATTGAATACTTTGGCCAGA
TCAGCCCCTTTGAAGGGATCACTAATTTAGGAAAGAAGAACAACAAACCATCATTCACTT
TCCTGCAGGTTCATCGTTTTCCTAATTATTTCTATGGATCCTGCTTTATTCTTTCTGTAA
ATTAAGGGGCAGGAGGAGAGTTTCTATAATAGATCAGCAATGTCTGGTTCTTATCCAAAT
ATTCCACCTATTAAGGATGTAAATTCTCATGGATTGGACAATCACTCTGCAACATTCCTG
AGAATTGAATAATATAATAATCTTGAAAGTCAGCAGAGTGGATTATCCACTTTTTTTTTC
TGGACTTGAACTTGTGAACTCAACAGTAGCACTGCAAAAGAGCAAATGTGCTAAGCACTT
TGCCAGAGTAACCTTCCATGTAGACTTTTCATCTTAAATACACACAACTGAAAACAACTA
CAATTTTTGGAAAATTTTGTACAAACCCGATACTTCTTTTGATTACATATAAATACAAAT
TAGCTATTTTTTTCCTAAAAAGTGGTTATAATAGTAAATAAATACAAAATAAATCTGACC
ATTATACTTCATGTGCTGGGGTTGAACCCATATAAAATGTACAACTAAATACATTTTAAA
TCTTTAAGGAATAATTCTCTGATTAAAATATTTGTTTTCCCAACTTCTTTTCGTAGATAT
AAATATATTTTCAAAATAGCTGTTTTTTTTTCCATTCCATTCCATAAATAAAGTCTTCAT
TGGGAAATATTAAAGTGTCAACTGGGGTGGGGTTTTTTTGTTTGTTTGTTTTTTTCTTTT
TTCTAAAATATATATATATATATATATTTTAGAAAAAAGAAAAAAACAAACAAACAAAAA
AACCCCACCCCAGTTGACACTTTAATATTTCCCAATGAAGACTTTATTTATGGAATGGAA
TGGAAAAAAAAACAGCTATTTTGAAAATATATTTATATCTACGAAAAGAAGTTGGGAAAA
CAAATATTTTAATCAGAGAATTATTCCTTAAAGATTTAAAATGTATTTAGTTGTACATTT
TATATGGGTTCAACCCCAGCACATGAAGTATAATGGTCAGATTTATTTTGTATTTATTTA
CTATTATAACCACTTTTTAGGAAAAAAATAGCTAATTTGTATTTATATGTAATCAAAAGA
AGTATCGGGTTTGTACAAAATTTTCCAAAAATTGTAGTTGTTTTCAGTTGTGTGTATTTA
AGATGAAAAGTCTACATGGAAGGTTACTCTGGCAAAGTGCTTAGCACATTTGCTCTTTTG
CAGTGCTACTGTTGAGTTCACAAGTTCAAGTCCAGAAAAAAAAAGTGGATAATCCACTCT
GCTGACTTTCAAGATTATTATATTATTCAATTCTCAGGAATGTTGCAGAGTGATTGTCCA
ATCCATGAGAATTTACATCCTTAATAGGTGGAATATTTGGATAAGAACCAGACATTGCTG
ATCTATTATAGAAACTCTCCTCCTGCCCCTTAATTTACAGAAAGAATAAAGCAGGATCCA
TAGAAATAATTAGGAAAACGATGAACCTGCAGGAAAGTGAATGATGGTTTGTTGTTCTTC
TTTCCTAAATTAGTGATCCCTTCAAAGGGGCTGATCTGGCCAAAGTATTCAATAAAACGT
AAGATTTCTTCATTATTGATATTGTGGTCATATATATTTAAAATTGATATCTCGTGGCCC
TCATCAAGGGTTGGAAATTTATTTGTGTTTTACCTTTACCTCATCTGAGAGCTCTTTATT
CTCCAAAGAACCCAGTTTTCTAACTTTTTGCCCAACACGCAGCAAAATTATGCACATCGT
GTTTTCTGCCCACCCTCTGTTCTCTGACCTATCAGCTTGCTTTTCTTTCCAAGGTTGTGT
GTTTGAACACATTTCTCCAAATGTTAAACCTATTTCAGATAATAAATATCAAATCTCTGG
CATTTCATTCTATAAAGTCCAACATGTAAGAGAA
Blat the sequence and select the browser for either match. Notice the alignment of each end of the sequence to the same loci, ending at a simple repeat.
Example 9
>c24_g1_i1 len=1895 path=[6161:0-730 6959:731-733 1263:734-757 1287:758-1894]
AAAATTAGCCAGGCGTGGTGGCACATGCCTTTAGTTCACACTACTTGGGAGGCTGAGATG
AGAATCACTTGAACCCGGGAGGTGCAGGTTAGAGTGAGCTGAGATTTGTGCCACTGACCT
CCAGCCTGGGAGACAGAGCAAGACACTGTCTCAAAAATAATAATAAGGACGTCCACCACA
CTTTACCTACCAAAATGCCCATTCCCCAAAGATGATTGCTGTTGAACGATTAGGGTACCT
TTCCTGATTTTTTTTGTCTAAGCACATTTAAAAACCAAGACTTTTGGTTTTGAGCGATAG
CTCTGAATCTCCTTTAGGTATGAAGTGTAGGAAATTGTATTTCTGCAGCAAACTTAGGCT
TTGCAACATCAAGTGTGGATTCACTGGAAATTATTTGAAGGAACACATAGCGATCATAAT
AGCCAAAAAATGTTGGGAAATGAAAAAGGGTGGGTTTTTTTAATTAAAAAAAAATTTTTT
TTTTTAAGAGACAGGTTCTTCGCTCCATCACCCAGGATGGAGTACAGTGGCGCGATCATA
GCTCACTGAAGGCTCAAACTCCTGGGCTCAAGCAATCCTGCCTCAGCCTCCCAAGAAGCT
AGGACTACAGGTGTGCACCACCATGCCTAGCTAATGTTTTAATATTTTGTAGAGATGGGG
TCTTGCTGTGTTGCCCTGGCTGGCCTCAAACACCTGGCCTCAAGCAATACAACCACCTCA
GCCTCCCACAGTCCTGGGATTACAGGCATGAGCCACCATGCCCGGCCCCTTATTTTACTT
TATCCTCCTGATTATTTGAATTTGTTACACTAAGCATGTATTTTATAATCAAAAATAATT
AAGATTTAAAACAATGTATTTGACTACTAAAAAGCAAATTATATAAATCAGTTGAATAAT
AATGTTGTTAAAGAGGCTGTTTAGCACTAATTTGACCAAATCTATAGTCAAAGTTTGATT
CTACTTGAATTTTTTGGAAATTTGCTGTTGTATTACTTATTCTTTGCCTTGTTCTCTGTG
AAGTCCTTTCCTAAAAAAGAAACTTATACAATTTAGTTCACAAAACTTTGTTGACCTCTT
TCTCTGTAGAAATGAAAACTAAATATATATAATTGAGAAATAATTCTGATACTCTTCATT
CCTATAAAAGTAATTAAGATAGACCTATAGGATTGTTGAACTTTGCTGCCAAATATAGTA
ACCAGTAACCACAGCTAGCTGTAAAATTGAAAATTCAGTTCAGTCAAACTAGCCATATTT
CAAGTGCTCAACAGCCACTGGTGGCTATTGGTTACCTTACTGACCAGCCAATATAGGCTA
TTTCCGTCATTATAGAAAGCTCTATTGGACAACATTGGTCTAGGACATATATTTTGTATT
TTCCCCTCACCCACCATCCAATAATGAGTAATAGCACAAAGTAAAAGTGACTTAATTTGA
AATTACTTCTGTTTGGCTAGTTTGCTTAGCTGATCACCACCAACATCATAGGTCTATAAA
TCACCCAACTAAGATCAGGGGTGTTTCATGGGAAAATCTACACAAACTATTCATTAAAAA
CCATAGAGCCATGGACTGTCATTTCTGATTTCTGTTTGATTCTTTGTGGTAATCATTGAA
TATACAGGGGCCTCTATACACTCTGGGGAGTATCTATTCTCAGGTGAGCAAAATACCGAA
TACTGAATGGAAATCAACTGTAAGTATTAGGACTTCATATGCAACTTGAATTTTTGGTGC
TGTCCGGAGTCTAGAGCCCCACAATCTGCTTTGGTTACAGTTTATCCCTGTAGGATAAAT
GATCCATTTAACCATTCATCAGAGGTGCTGTAATTTTAAATTGTCTCTTGTCTCCTTCAG
TTAATTTTCAGAATTAAAAACATACCATGGGAAAA
Blat the sequence and select the browser for either match, then browse to chr20:18,467,148-18,469,269. Notice the alignment of each end of the sequence to the same loci, ending at a SINE repeat.
Example 10
>c19_g1_i1 len=2433 path=[2765:0-2432]
GATCACCTGAGGTCAGGAGTTCGACACCAGCCTGGCCAATGTGGTGAAACCCCATGTCTA
CTAAAAATACAAAAAAATTAGCCAGGCATGGTGGTGTACGCCTGTAATCCCAGCTATTCT
GGAGGCTGAGGCAGGAGAATTGTTTGAATCCAGGAGATGGAGGTTGCAGTGAGCTGAGAT
CGTGCCATTGCACTCCAGCATGGGCAACAGGGCAAGACTCCGTCTCAAAAAAAAGAAAAA
GAGCTGGGGCTGTTGTCCTCAATGGGGGACATTTGAGGACCTAGACTGTCCGAAGTCTTT
CTCTTTGCTCTGGAGGTCACATAGAGCCTGGACCATCCAAGATCTGCTGCTACGGTAAGA
CATCATCTCAGCTTTCCTTTCCCTTCTAGGCCACAGTCCTACCTTCTGAGGTATGGTGGT
GGTCTCAACGAGACTTGTAGATTTTCTGAAAATGACTTTCTCGTTGACTCTAGGGGTTGT
TTCTACCTTGTGGGTGGGGCCTGGTTAATGGTGGGGATGTAGAATGGGGCTCAACAGGCA
GGGCATCCAGATGGTACTGGAAACCCCAAACTCAAGAACTAACTAGGTCAGACCCCCCAG
GAGGCTTATTCTCTTTTTGGAACCCTGGCCCTGGTCCCACCTTCTCTGCACTCGCACTAG
AGGTCGCAGGTGGGATCATGGCACTGGAAGGAAGTAGGTGACTTCTAAGGGCTAAGAGAG
GAAAGAGCAAGGGTACAGGTGGGACCCTAGATGCACCTCTGTGTCCCACCCTCCCTCCCT
GAGTGCACAGCCTTGCCTCTGGGGTGCCCAGGAGGCTGAATTGGGGTTCTAGGTGTGCAG
CCTTGGTTTCCCTTTTGGCCTCTCCTTTGGGCCTAGGCATCATCCAAAGAGACAGCCTCG
TCATTCAGGCTGATGTAGAAGCTGAGGGACTCCCGGAGACCCTCACTGAGAAGAGACTCC
TCCCCTGTGGCAGCTTCAGAAAACAGGAGGGACTGTCCAGCTCTTTCCAGTTGAGTGGTG
TCCTCTGCACAGTCACAGGTAGGGGTATATCCTTGCCAGGGAGCGGGCCAGCCCTCTGCA
GGACACAGGGCTCCTTGAGTAGGCAGCAGATGTCATCCGCCAGCCAGAGTAATGGTCCAC
CAGGGCCTGGAGTGAGGGGAAGGTGAGGCGCGGTGAGATGTACAGCCAGCCATTGTCAAG
GCAGTGGATCCTGTAGTGTCTGATCCGGTCCCAGGATGCAGGGCGGCTGAGGCGGACTGA
CAGAGAGTAAGAGCTCTCCTGGTCTGGCTCTCCCGGATGAGGAAGGCCCCTCCAGGGTTC
CCAGGTAACAACATCAGTTCCTCTGGTTTCTCCCTGCTCAGGCCCTCATACAGCCACCAT
GGGAGACTTTGGCCACGTGGACGCTGGGGATGTTATACTCTCTGCCTGAGACTTCAGACA
GCACCGTCCACCAGTCTCCATCTCAGAGACGATGGTCAATGGCTCCCCGAGTCTCAGCGA
CAGCTCGGGCGGGCCACCTGCCGGGAAACTGCCCAGGGCCACGGCTGTGGCCTTGCTTCT
CCTGCTTCCATGGTCACAGGTCCCTGGCCTTGGACAGAGGAACTCAAGCTTGGGCTTGGC
AGAGATTTTCTTCTGCTGGGCAGACTTCCCATTGTTCCTCAGCAGAGCACTCAGAAGCAC
ATCATCGAGGGAAATTGCTGGGAGGGCCGGTAGGGCGCCATGGGCCGCTGCCCCATCATG
CTGCTCCCCTGGCTGCCCTGCCCCATCATGGCGATGGACGACTGGCCCTGGTAGTGCTGG
CTGCCGCCCTGCGCCGAGCTGTAGTGCGACGTGGCCGCCTGCTGCTGCATCATGGAGATG
GGTTGGACTGCATGTTGATGTTGGTCCGAGACACGTAGTTGCCGATGGTGCCTTGCCCCT
GCATGGGGACGTCCTGCGAGGCGGGTCCGGCGTGGCTGTAGCCGGGCCCAGAGATGCTCA
TGGAGGTGGTGGGCAGCGTGTTAGGCGCCGTCTGCTGCATGGACACGTGGCTCGGCCGTT
GCCAATCTGGCCCTGCAGGAGGGAGGAGGGTGGCAGGCCCGTGCGGATGGCGTCACTCAG
GCTGCCCTGAGAGTGCAGGCCCTGGCTGGAGCCGCTCTGAGTCAGGGCTCCAGGGCCCAG
GTTCATGTTCTGCGTGGGCGGGCAGGAAGCAGGGACTGCATGTTCTGGTTGGAGTCTGCG
ATCGTGGCCAGGTATACCAGGTTCCGGTGCAGGATCTGCTGGTACGCGTGCACTCGGCCG
TCTTGCCCTTGCTCTGGTACTCCAGGATGCACTGGATCAGGTGGTGGTTCTCGTCCAGCA
TTTCTGGATGGTTTGCTGCGTAACCTCCCCTTTGCCTCTTGGCCGGGCAGACGCGAAGGC
CACGGACATGGTGGCGGCGCGGGGCTCAGCCCG
Blat the sequence and select the browser for either match, then browse to chr20:35,241,397-35,269,781 and chr20:60,718,853-60,738,677. Notice the alignment of each end of the sequence to the same loci, ending at a SINE repeat.