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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC

Basic information

species Physcomitrella patens
transcript PP1S49_256V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                                                 |  || |  ||| |  |||| |      |   |  | || |  | ||    |  |||| |      |||  ||   |||    || |  | ||    | ||| || ||| |||||||||| ||||| || ||||| ||||| || |||||||| ||||||||||| |||||||| ||||| ||||| |||||||| || |||
------------------------------------------------------------------------------------------------ttccacatatgttgt-ttgcattgcacttgtgtgatgctgttcttgaagtaattatattatcaattggattgtattgtttctcatcctg-tgtat-catacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcga-aggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggt-cataatatacatg-tgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                                                   | | |  |  || ||  |  ||  | ||   | |  | ||  ||  | |   ||   |    |    |  | ||| | |   | |||   |    |  ||||| || ||| | |||||||| || || || ||||| ||||| || || |||||||| || ||||| ||||||||||| |||||||| || ||||| || || 
--------------------------------------------------------------------------------------------------agtcatatgcctt-ctatatcatatatagtttgtatgtcattgttctaggtctgt---tgaaccactgtactcactgtataaattcatctcacgtttaatgcagTGTTGATCGGAACAAGTACCAGATTCAAATTCCTTTGCCACCCAAAATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATAT

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                                        ||  || | |    |  || | | ||    | |  |  |||  || |||   ||      |   |  | ||  || |  ||     | ||   | || |     | ||||| || ||| | |||||||| || || || || ||  | || || || |||||||| || ||||| |||||||| |||||||||||||||||||| || |||
---------------------------------------------------------------------------------------ttcggttatttctctgcgcgctgtgcta---tttttaccgaataagttgaacctt-----ttcccacctagt--gaaaactttgtgatctcacacgta-tgcttgt-tgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGACCCAAGTGTTACCATGATGACCGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                                        |   || | |   | |  ||| | ||    |  |  |   ||  ||   || ||   | || ||     |    |  | ||| ||   | | |  |  |       ||||| || ||| | |||||||| || || || || ||  | || || || |||||||| || ||||| |||||||| |||||||||||||||||||| || |||
--------------------------------------------------------------------------------------ttttggttatttctccatgtgttgtgctattattcccgaatgagttga-actgtttctcacctagt-----gaaaaaactattatctcactggattcttgt-------tgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                      || || || | |  |   | |||| |   || |||    | | | || | | ||  |||| ||  | |  |  |    || |||  |||  |     ||  ||   |       | |  |    | |||||| ||||||||||| ||||| || || |||||| ||||||| || |||||||| || ||||| ||||||||||| || || ||||| ||||| || || 
---------------------------------------------------------------------gtatgt-tccaatcag---taactttt---gatgttaaaat-attcca-tgttgagagaagaagg-ggtattctag---tgttatgctgtctgc----ttgtctgactgaacttcattgcatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCTAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                      || || || | |  |   | |||| |   || |||    | | | || | | ||  |||| ||  | |  |  |    || ||| ||||  |     ||  ||   |       | |  |    | |||||| ||||||||||| ||||| || || |||||| ||||||| || |||||||| || ||||| ||||||||||| || || ||||| ||||| || || 
---------------------------------------------------------------------gtatgt-tccaatcag---taactttt---gatgttaaaat-attcca-tgttgagagaagaagg-ggtattctag---tgttatgttgtctgc----ttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttt--tactgcagtatcga-aggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                                          |  | ||       |  |||  | |   | |||  | || ||| ||| ||    |    ||  ||  | || | |  || || || ||      |||  ||| ||| |||||||| ||||||||||| ||||| || |||||||| |||||||| || ||||| || || || || |||||||| || || || ||||||||||| || || 
----------------------------------------------------------------------------------------gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaat-ttgacctt------cattttat-cat-tgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                                  |  |||||   |   |        | |  | || |  | |  || ||| ||| ||    ||    || ||  | || | |     || || ||      |||  ||| ||| |||||||| |||||||| || ||||| || |||||||| |||||||| || ||||| || || || || |||||||| || || || ||||||||||| || || 
---------------------------------------------------------------------------------gtatgcctccaataagtaatttgatgctagaatgtataaccatagaaagaagaggaactctatggccttgttgtatgcttgtttgtttgacctt------cattttat-cat-tgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT

upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 5
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                                                                                                                                            |       |  | || |||||  ||||| ||     |   ||    | | |   | ||| || ||||| ||||| ||||| ||||| || || ||||| ||||||||||| || ||||| || |||||||| |||||||| ||||| ||||| || |||
-------------------------------------------------------------------------------------------------------------------------------------------gtatggtttttttcttatgttctcgatgtaaatgacatt--tctgtgtgttctattacagTGTTGATAGGAACAAATATCAGATCCAAATACCTTTGCCCCCTAAGATTGATCCGAGCGTCACTATGATGACGGTGGAGGAGAAGCCCGATGTAACTTAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208386966|gb|DC956935.1|DC956935
EST:     ACAGACATAGAGGAGGGCATGCGTGTTTGG                         GGTAGATAGAAACNAGTATCGAATCCAGATTCCATTGCCTCCTAAGATTG
genomic: ACAGACATAGAGGAGGGCATGCGTG-TTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTG
EST: gi|67717642|gb|BJ967901.1|BJ967901
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|208348229|gb|DC905485.1|DC905485
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100393232|gb|BY989787.1|BY989787
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|67507498|gb|BJ940380.1|BJ940380
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100442037|gb|BY962930.1|BY962930
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|208384192|gb|DC911300.1|DC911300
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGGTAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100435405|gb|BY979227.1|BY979227
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGGTGG                         GGTAGATAGAAACAAGTATCAA-TCCAGATTCCATTGCCTTCCTA-GATTG
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCT-CCTAAGATTG
EST: gi|208375716|gb|DC936656.1|DC936656
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCGAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100445251|gb|BY982880.1|BY982880
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|67716993|gb|BJ967252.1|BJ967252
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100441014|gb|BY962502.1|BY962502
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100385842|gb|BY951036.1|BY951036
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|208397607|gb|DC912225.1|DC912225
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|208387130|gb|DC941302.1|DC941302
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100355304|gb|BY965094.1|BY965094
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGN                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAAGAT-G
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAA-GATTG
EST: gi|67704545|gb|BJ964778.1|BJ964778
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100352668|gb|BY945387.1|BY945387
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|18361561|gb|BJ193627.1|BJ193627
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|67719122|gb|BJ969381.1|BJ969381
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA
EST: gi|100417415|gb|BY957319.1|BY957319
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGGAT-G
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAG-ATTG
EST: gi|100352747|gb|BY945428.1|BY945428
EST:     TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGG                         GGTAGATAGAAACAAGTATCANATCCAGATTCCATTGCCTCCTAAGATTGA
genomic: TTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 35 (downstream exon)
Score: 12

TTTGTCGTTGGATTGGGCGAGAAGGTGTCTCCAACAGACATAGAGGAGGGCATGCGTGTTGGgtacgttttc ... acatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC
                     tgttaac  putative branch site (score: 12)
                                      ataatatacat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
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