CLUSTAL W (1.83) multiple sequence alignment
transcript2 GCCTTCCTGGGATTGGAGTCTCGAGCTTTCTTCGTTCGTTCGTCGGCGGGTTCGCGCCCT 60
transcript3 GCCTTCCTGGGATTGGAGTCTCGAGCTTTCTTCGTTCGTTCGTCGGCGGGTTCGCGCCCT 60
transcript1 GCCTTCCTGGGATTGGAGTCTCGAGCTTTCTTCGTTCGTTCGTCGGCGGGTTCGCGCCCT 60
************************************************************
transcript2 TCTCGCGCCTCGGGGCTGCGAGGCTGGGGAAGGGGTTGGAGGGGGCTGTTGATCGCCGCG 120
transcript3 TCTCGCGCCTCGGGGCTGCGAGGCTGGGGAAGGGGTTGGAGGGGGCTGTTGATCGCCGCG 120
transcript1 TCTCGCGCCTCGGGGCTGCGAGGCTGGGGAAGGGGTTGGAGGGGGCTGTTGATCGCCGCG 120
************************************************************
transcript2 TTTAAGTTGCGCTCGGGGCGGCCATGTCGGCCGGCGAGGTCGAGCGCCTAGTGTCGGAGC 180
transcript3 TTTAAGTTGCGCTCGGGGCGGCCATGTCGGCCGGCGAGGTCGAGCGCCTAGTGTCGGAGC 180
transcript1 TTTAAGTTGCGCTCGGGGCGGCCATGTCGGCCGGCGAGGTCGAGCGCCTAGTGTCGGAGC 180
************************************************************
transcript2 TGAGCGGCGGGACCGGAGGGGATGAGGAGGAAGAGTGGCTCTATGGCGGCCCATGGGACG 240
transcript3 TGAGCGGCGGGACCGGAGGGGATGAGGAGGAAGAGTGGCTCTATGGCGGCCCATGGGACG 240
transcript1 TGAGCGGCGGGACCGGAGGGGATGAGGAGGAAGAGTGGCTCTATGGCG------------ 228
************************************************
transcript2 TGCATGTGCACAGTGATTTGGCAAAGGACCTAGATGAAAATGAAGTTGAAAGGCCAGAAG 300
transcript3 TGCATGTGCACAGTGATTTGGCAAAGGACCTAGATGAAAATGAAGTTGAAAGGCCAGAAG 300
transcript1 ---------------------------------ATGAAAATGAAGTTGAAAGGCCAGAAG 255
***************************
transcript2 AAGAAAATGCCAGTGCTAATCCTCCATCTGGAATTGAAGATGAAACTGCTGAAAATGGTG 360
transcript3 AAGAAAATGCCAGTGCTAATCCTCCATCTGGAATTGAAGATGAAACTGCTGAAAATGGTG 360
transcript1 AAGAAAATGCCAGTGCTAATCCTCCATCTGGAATTGAAGATGAAACTGCTGAAAATGGTG 315
************************************************************
transcript2 TACCAAAACCGAAAGTGACTGAGACCGAAGATGATAGTGATAGTGACAGCGATGATGATG 420
transcript3 TACCAAAACCGAAAGTGACTGAGACCGAAGATGATAGTGATAGTGACAGCGATGATGATG 420
transcript1 TACCAAAACCGAAAGTGACTGAGACCGAAGATGATAGTGATAGTGACAGCGATGATGATG 375
************************************************************
transcript2 AAGATGATGTTCATGTCACTATAGGAGACATTAAAACGGGAGCACCACAGTATGGGAGTT 480
transcript3 AAGATGATGTTCATGTCACTATAGGAGACATTAAAACGGGAGCACCACAGTATGGGAGTT 480
transcript1 AAGATGATGTTCATGTCACTATAGGAGACATTAAAACGGGAGCACCACAGTATGGGAGTT 435
************************************************************
transcript2 ATGGTACAGCACCTGTAAATCTTAACATCAAGACAGGGGGAAGAGTTTATGGAACTACAG 540
transcript3 ATGGTACAGCACCTGTAAATCTTAACATCAAGACAGGGGGAAGAGTTTATGGAACTACAG 540
transcript1 ATGGTACAGCACCTGTAAATCTTAACATCAAGACAGGGGGAAGAGTTTATGGAACTACAG 495
************************************************************
transcript2 GGACAAAAGTCAAAGGAGTAGACCTTGATGCACCTGGAAGCATTAATGGAGTTCCACTCT 600
transcript3 GGACAAAAGTCAAAGGAGTAGACCTTGATGCACCTGGAAGCATTAATGGAGTTCCACTCT 600
transcript1 GGACAAAAGTCAAAGGAGTAGACCTTGATGCACCTGGAAGCATTAATGGAGTTCCACTCT 555
************************************************************
transcript2 TAGAGGTAGATTTGGATTCTTTTGAAGATAAACCATGGCGTAAACCTGGTGCTGATCTTT 660
transcript3 TAGAGGTAGATTTGGATTCTTTTGAAGATAAACCATGGCGTAAACCTGGTGCTGATCTTT 660
transcript1 TAGAGGTAGATTTGGATTCTTTTGAAGATAAACCATGGCGTAAACCTGGTGCTGATCTTT 615
************************************************************
transcript2 CTGATTATTTTAATTATGGGTTTAATGAAGATACCTGGAAAGCTTACTGTGAAAAACAAA 720
transcript3 CTGATTATTTTAATTATGGGTTTAATGAAGATACCTGGAAAGCTTACTGTGAAAAACAAA 720
transcript1 CTGATTATTTTAATTATGGGTTTAATGAAGATACCTGGAAAGCTTACTGTGAAAAACAAA 675
************************************************************
transcript2 AGAGGATACGAATGGGACTTGAAGTTATACCAGTAACCTCTACTACAAATAAAATTACGG 780
transcript3 AGAGGATACGAATGGGACTTGAAGTTATACCAGTAACCTCTACTACAAATAAAATTACGG 780
transcript1 AGAGGATACGAATGGGACTTGAAGTTATACCAGTAACCTCTACTACAAATAAAATTACGG 735
************************************************************
transcript2 CCGAAGACTGTACTATGGAAGTTACACCAGGTGCAGAGATCCAAGATGGCAGATTCAATC 840
transcript3 CCGAAGACTGTACTATGGAAGTTACACCAGGTGCAGAGATCCAAGATGGCAGATTCAATC 840
transcript1 ------------------------------------------------------------
transcript2 TTTTTAAGGTACAGCAGGGAAGAACTGGAAACTCAGAGAAAGAAACTGCCCTTCCATCTA 900
transcript3 TTTTTAAGGTACAGCAGGGAAGAACTGGAAACTCAGAGAAAGAAACTGCCCTTCCATCTA 900
transcript1 ---------TACAGCAGGGAAGAACTGGAAACTCAGAGAAAGAAACTGCCCTTCCATCTA 786
***************************************************
transcript2 CAAAAGCTGAGTTTACTTCTCCTCCTTCTTTGTTCAAGACTGGGCTTCCACCGAGCAGAA 960
transcript3 CAAAAGCTGAGTTTACTTCTCCTCCTTCTTTGTTCAAGACTGGGCTTCCACCGAGCAGAA 960
transcript1 CAAAAGCTGAGTTTACTTCTCCTCCTTCTTTGTTCAAGACTGGGCTTCCACCGAGCAG-- 844
**********************************************************
transcript2 ACAGCACTTCTTCTCAGTCTCAGACAAGTACTGCCTCCAGAAAAGCCAATTCAAGCGTTG 1020
transcript3 ACAGCACTTCTTCTCAGTCTCAGACAAGTACTGCCTCCAGAAAAGCCAATTCAAGCGTTG 1020
transcript1 ------------------------------------------------------------
transcript2 GGAAGTGGCAGGATCGATATGGGAGGGCCGAATCACCTGATCTAAGGAGATTACCTGGGG 1080
transcript3 GGAAGTGGCAGGATCGATATGGGAGGGCCGAATCACCTGATCTAAGGAGATTACCTGGGG 1080
transcript1 ----------------------------------------------GAGATTACCTGGGG 858
**************
transcript2 CAATTGATGTTATCGGTCAGACTATAACTATCAGCCGAGTAGAAGGCAGGCGACGGGCAA 1140
transcript3 CAATTGATGTTATCGGTCAGACTATAACTATCAGCCGAGTAGAAGGCAGGCGACGGGCAA 1140
transcript1 CAATTGATGTTATCGGTCAGACTATAACTATCAGCCGAGTAGAAGGCAGGCGACGGGCAA 918
************************************************************
transcript2 ATGAGAACAGCAACATACAGGTCCTTTCTGAAAGATCTGCTACTGAAGTAGACAACAATT 1200
transcript3 ATGAGAACAGCAACATACAGGTCCTTTCTGAAAGATCTGCTACTGAAGTAGACAACAATT 1200
transcript1 ATGAGAACAGCAACATACAGGTCCTTTCTGAAAGATCTGCTACTGAAGTAGACAACAATT 978
************************************************************
transcript2 TTAGCAAACCACCTCCGTTTTTCCCTCCAGGAGCTCCTCCCACTCACCTTCCACCTCCTC 1260
transcript3 TTAGCAAACCACCTCCGTTTTTCCCTCCAGGAGCTCCTCCCACTCACCTTCCACCTCCTC 1260
transcript1 TTAGCAAACCACCTCCGTTTTTCCCTCCAGGAGCTCCTCCCACTCACCTTCCACCTCCTC 1038
************************************************************
transcript2 CATTTCTTCCACCTCCTCCGACTGTCAGCACTGCTCCACCTCTGATTCCACCACCGGGTT 1320
transcript3 CATTTCTTCCACCTCCTCCGACTGTCAGCACTGCTCCACCTCTGATTCCACCACCGGGTT 1320
transcript1 CATTTCTTCCACCTCCTCCGACTGTCAGCACTGCTCCACCTCTGATTCCACCACCGGGTT 1098
************************************************************
transcript2 TTCCTCCTCCACCAGGCGCTCCACCTCCATCTCTTATACCAACAATAGAAAGTGGACATT 1380
transcript3 TTCCTCCTCCACCAGGCGCTCCACCTCCATCTCTTATACCAACAATAGAAAGTGGACATT 1380
transcript1 TTCCTCCTCCACCAGGCGCTCCACCTCCATCTCTTATACCAACAATAGAAAGTGGACATT 1158
************************************************************
transcript2 CCTCTGGTTATGATAGTCGTTCTGCACGTGCATTTCCATATGGCAATGTTGCCTTTCCCC 1440
transcript3 CCTCTGGTTATGATAGTCGTTCTGCACGTGCATTTCCATATGGCAATGTTGCCTTTCCCC 1440
transcript1 CCTCTGGTTATGATAGTCGTTCTGCACGTGCATTTCCATATGGCAATGTTGCCTTTCCCC 1218
************************************************************
transcript2 ATCTTCCTGGTTCTGCTCCTTCGTGGCCTAGTCTTGTGGACACCAGCAAGCAGTGGGACT 1500
transcript3 ATCTTCCTGGTTCTGCTCCTTCGTGGCCTAGTCTTGTGGACACCAGCAAGCAGTGGGACT 1500
transcript1 ATCTTCCTGGTTCTGCTCCTTCGTGGCCTAGTCTTGTGGACACCAGCAAGCAGTGGGACT 1278
************************************************************
transcript2 ATTATGCCAGAAGAGAGAAAGACCGAGATAGAGAGAGAGACAGAGACAGAGAGCGAGACC 1560
transcript3 ATTATGCCAGAAGAGAGAAAGACCGAGATAGAGAGAGAGACAGAGACAGAGAGCGAGACC 1560
transcript1 ATTATGCCAGAAGAGAGAAAGACCGAGATAGAGAGAGAGACAGAGACAGAGAGCGAGACC 1338
************************************************************
transcript2 GTGATCGGGACAGAGAAAGAGAACGCACCAGAGAGAGAGAGAGGGAGCGTGATCACAGTC 1620
transcript3 GTGATCGGGACAGAGAAAGAGAACGCACCAGAGAGAGAGAGAGGGAGCGTGATCACAGTC 1620
transcript1 GTGATCGGGACAGAGAAAGAGAACGCACCAGAGAGAGAGAGAGGGAGCGTGATCACAGTC 1398
************************************************************
transcript2 CTACACCAAGTGTTTTCAACAGCGATGAAGAACGATACAGATACAGGGAATATGCAGAAA 1680
transcript3 CTACACCAAGTGTTTTCAACAGCGATGAAGAACGATACAGATACAGGGAATATGCAGAAA 1680
transcript1 CTACACCAAGTGTTTTCAACAGCGATGAAGAACGATACAGATACAGGGAATATGCAGAAA 1458
************************************************************
transcript2 GAGGTTATGAGCGTCACAGAGCAAGTCGAGAAAAAGAAGAACGACATAGAGAAAGACGAC 1740
transcript3 GAGGTTATGAGCGTCACAGAGCAAGTCGAGAAAAAGAAGAACGACATAGAGAAAGACGAC 1740
transcript1 GAGGTTATGAGCGTCACAGAGCAAGTCGAGAAAAAGAAGAACGACATAGAGAAAGACGAC 1518
************************************************************
transcript2 ACAGGGAGAAAGAGGAAACCAGACATAAGTCTTCTCGAAGTAATAGTAGACGTCGCCATG 1800
transcript3 ACAGGGAGAAAGAGGAAACCAGACATAAGTCTTCTCGAAGTAATAGTAGACGTCGCCATG 1800
transcript1 ACAGGGAGAAAGAGGAAACCAGACATAAGTCTTCTCGAAGTAATAGTAGACGTCGCCATG 1578
************************************************************
transcript2 AAAGTGAAGAAGGAGATAGTCACAGGAGACACAAACACAAAAAATCTAAAAGAAGCAAAG 1860
transcript3 AAAGTGAAGAAGGAGATAGTCACAGGAGACACAAACACAAAAAATCTAAAAGAAGCAAAG 1860
transcript1 AAAGTGAAGAAGGAGATAGTCACAGGAGACACAAACACAAAAAATCTAAAAGAAGCAAAG 1638
************************************************************
transcript2 AAGGAAAAGAAGCGGGCAGTGAGCCTGCCCCTGAACAGGAGAGCACCGAAGCTACACCTG 1920
transcript3 AAGGAAAAGAAGCGGGCAGTGAGCCTGCCCCTGAACAGGAGAGCACCGAAGCTACACCTG 1920
transcript1 AAGGAAAAGAAGCGGGCAGTGAGCCTGCCCCTGAACAGGAGAGCACCGAAGCTACACCTG 1698
************************************************************
transcript2 CAGAATAGGCATGGTTTTGGCCTTTTGTGTATATTAGTACCAGAAGTAGATACTATAAAT 1980
transcript3 CAGAATAGGCATGGTTTTGGCCTTTTGTGTATATTAGTACCAGAAGTAGATACTATAAAT 1980
transcript1 CAGAATAGGCATGGTTTTGGCCTTTTGTGTATATTAGTACCAGAAGTAGATACTATAAAT 1758
************************************************************
transcript2 CTTGTTATTTTTCTGGATAATGTTTAAGAAATTTACCTTAAATCTTGTTCTGTTTGTTAG 2040
transcript3 CTTGTTATTTTTCTGGATAATGTTTAAGAAATTTACCTTAAATCTTGTTCTGTTTGTTAG 2040
transcript1 CTTGTTATTTTTCTGGATAATGTTTAAGAAATTTACCTTAAATCTTGTTCTGTTTGTTAG 1818
************************************************************
transcript2 TATGAAAAGTTAACTTTTTTTCCAAAATAAAAGAGTGAATTTTTCATGTTAAGTTAAAAA 2100
transcript3 TATGAAAAGTTAACTTTTTTTCCAAAATAAAAGAGTGAATTTTTCATGTTAAGTTAAAAA 2100
transcript1 TATGAAAAGTTAACTTTTTTTCCAAAATAAAAGAGTGAATTTTTCATGTTAAGTTAAAAA 1878
************************************************************
transcript2 TCTTTGTCTTGTACTATTTCAAAAATAAAAAGACAGCAATGACTTTATATCCAA 2154
transcript3 ------------------------------------------------------
transcript1 TCTTTGTCTTGTACTATTTCAAAAATAAAAAGACAGCAATGACTTTATATCCAA 1932
Here we can see the alignment between the three transcripts of FIP1L1. As we have said before, the transcript number 1 doesn't have exons number 2, 9 and 11. We have marked in green the place where transcript 2 and 3 have exon 2 and transcript number 1 hasn't; in red the place where transcript 2 and 3 have exon 9 and transcript number 1 hasn't; and finally, in blue the place where transcript 2 and 3 have exon 11 and transcript number 1 hasn't. In yellow we have marked the absence of 54 nucleotides in transcript number 3, wheareas transcript number two has this 54 nucleotides.