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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG

Basic information

species Physcomitrella patens
transcript PP1S372_38V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTA-AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                              |   |||  |  | |||||   | |      ||| |  |  |||  |  |  ||       ||   |  | |  |    |   |          |    ||  |   |||||||||||||||||  |||||||| | || |||||||||||| |||||||||| |||
------------------------gcatgcacattcaaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagCAGTTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G110378_T03 (Zea mays), 3'ss of exon 2
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGA--GCAGGTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                       ||   | ||  |   || | ||   |   |        |  | |      |   |      | |  ||| |    |  ||   ||  |  | |    |||| ||     | |   |||||||||||||||||  |||||||| | || |||||||||||| |||||||||| |||
-----------------------caaatccagtcttccttttcattcacatgttgaactaaaacactttcatcactggttggtatttgattc-tatccatatgccacattgccgcttgctgcagTTCT----TTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G110378_T01 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgct---tagGTGTTGCAAAGTGGTTGA--GCAGGTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                                  ||     |    ||| | |   |||   |||  ||              | ||||||  | ||    |  ||   ||  |  | |    |||| ||     | |   |||||||||||||||||  |||||||| | || |||||||||||| |||||||||| |||
---------------------------------gtcttccttttcattcacatg--ttgaactaaaacactttcatcactggttggtatttgattctatccatatgccacattgccgcttgctgcagttct----ttagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G067985_T12 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTA-AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                              |   |||  |  | |||||   | |      ||| |  |  |||  |  |  ||       ||   |  | |  |    |   |          |    ||  |   |||||||||||||||||  |||||||| | || |||||||||||| |||||||||| |||
---------------------------tgcacattcaaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagTTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTA-AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                                   ||  |  | |||||   | |      ||| |  |  |||  |  |  ||       ||   |  | |  |    |   |          |    ||  |   |||||||||||||||||  |||||||| | || |||||||||||| |||||||||| |||
-----------------------------------caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G104017_T04 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactag-gatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
             || |  ||  ||   | || | ||  ||  |||       |    |   | | ||  | |     |||  |||  |||   | | || | |   |       |  ||||| ||   |  ||    ||||||||||||||||  |||||||| | || |||||||||||| | |||||||| |||
-------------atgcgtct--caaatccagtgctccttttcaatcacatattgaactaaaacactt--tcatcattgactcatttgattctatccatatgcgccacc------tgcagcagTTCTGTAGAAA----TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G053284_T01 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcct--cccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
    || || | | | || |  |   | |  |  ||  ||||   |||  |||  | |   ||| | || |   |  || ||  | | ||    |   |    || |||| |                  ||| |   |||||||| |   |||| ||||||||  | ||||||||||||||| ||||||||||||||
---ggtttacc-attgcagcggcggcggcatgcttcttttgtggggtttacctgactccatggacactttaacgattaacaccgagtata----gcattc---tgctgcagAAC----------------ACTGAGGAATGGCTGAAG---AGGATGTCCAGCCCCTTGTGTGCGACAATGGCACTGGAATGGTTAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G067985_T04 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTA-AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                              |   |||  |  | ||||    | |  |   ||| |  |  |||  |  |  ||        |   || | | ||    |   |          |    ||  |   |||||||||||||||||  |||||||| | || |||||||||||| | |||||||| |||
---------------------------tgcacattcaaatccagtgtttcttttcaatcacatagtgaactaaaacactctcatcactcagtgatatttgattttatccacatgccacttgcagcagTTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G067985_T02 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTA-AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                     ||| | ||     |||  |  | ||||    | |  |   ||| |  |  |||  |  |  ||        |   || | | ||    |   |          |    ||  |   |||||||||||||||||  |||||||| | || |||||||||||| | |||||||| |||
---------------------acctgcac---attcaaatccagtgtttcttttcaatcacatagtgaactaaaacactctcatcactcagtgatatttgattttatccacatgccacttgcagCAGTTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G104017_T03 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTA--AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                        || |   |  |||  |  | || ||   | |  |   ||| |  |  |||  |     ||  | |  |    ||   | |  | |  ||    | | |   ||       |   |||||||||||||||||  |||||||| | || |||||||||||| | |||||||| |||
------------------------agcatgcgtctcaaatccagtgctccttttcaatcacatattgaactaaaacactttcatcat-tgactcatttgattctatccatatgcgccacctgcagCAGTTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAG

upper sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G104017_T01 (Zea mays), 3'ss of exon 1
atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTA--AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                                   ||  |  | || ||   | |  |   ||| |  |  |||  |     ||  | |  |    ||   | |  | |  ||    | | |   ||       |   |||||||||||||||||  |||||||| | || |||||||||||| | |||||||| |||
-----------------------------------caaatccagtgctccttttcaatcacatattgaactaaaacactttcatcat-tgactcatttgattctatccatatgcgccacctgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAG

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|208377765|gb|DC940877.1|DC940877
EST:     CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCC--TTT-TT-A-                         ---TT-C--AGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG
genomic: CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCCTTTTTATTCAGgtaatacctg ... tcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG
EST: gi|100409313|gb|BY991949.1|BY991949
EST:     CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCC--TTT-TT-A-                         ---TT-C--AGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG
genomic: CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCCTTTTTATTCAGgtaatacctg ... tcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG
EST: gi|100417941|gb|BY993260.1|BY993260
EST:     CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCCTTTTTATTCAG                         GTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGACTGATGGTGAG
genomic: CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCCTTTTTATTCAGgtaatacctg ... tcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG
EST: gi|67703871|gb|BJ964104.1|BJ964104
EST:     CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCCTTTTTATTCAG                         GTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG
genomic: CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCCTTTTTATTCAGgtaatacctg ... tcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG
EST: gi|100380171|gb|BY968883.1|BY968883
EST:     CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCC--TTT-TT-A-                         ---TT-C--AGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG
genomic: CAGGCGCTTCTGAGCTCCATTTTTGCTTCTGCTCCGGCCTTTTTATTCAGgtaatacctg ... tcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
                                   aaattgtattt  TA-rich tract