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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagatcgtggtagttttgctcattaatacaatttttttggaacttttttttgtcatctttgctaaatttgttactgattgtgtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT

Basic information

species Zea mays
transcript GRMZM2G331032_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------cagatcgtgg---tagttttgctcattaatacaatttttttggaacttt-----tttttgtcatctttgctaaatttgttactgattgtgtcttctcttgc-tctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
                                    | || | |    | ||||| || |||| || | ||| | ||| |  |      | |||   |  ||  || ||||   | ||| | |  ||| || || | || |||| || ||||| || || ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||| || ||||||
gtatcactttatcaataattagtacatgaagaaaaaaaattgagcatctggtttttctgattagtatagtttatatggtatgtacacaatctttactactttaactgaattgtctgctggtcggttctcctttttcctcaacagCGGAAAGACCATTGAGCTTGATGATGTCACATTCCACCAGTGTGTCAACTTGACAAGATTTAACTCAGAAAAGACAGTCAGCTTTGTGCCGCCAGACGGT

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 7
cagatcgtggtagttttgctcattaatacaatttttttggaacttttttttgtcatctttgctaaatttgttactgattgtgtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
            || |   |  ||||||||     ||    |    |         |||| ||    ||||  || | ||  |||  | |||   | |||||| || || || || ||||||||||||||||| ||||||||||| ||| | || ||||| ||||| || ||||| || ||||| || ||||| || || 
------------gtatacgttgttaataca-----ttgaacatcagtagccactgacttttct----ttgt-gctaactgactctcgttttg---tgcagTGGTAAAACCATTGAGCTTGATGATGTCACATTTCACCAGTGTGTGAACCTGACCAGATTCAACTCCGAGAAGACTGTTAGTTTTGTACCACCGGATGGA

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 7
cagatcgtggtagttttgctcattaatacaatttttttgga--acttttttt----tgtcatctttgctaaatttgttactgattgt---gtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
           ||||||| | || |  | | || |||   |   ||| ||||    ||| || || | | | ||  | ||| | | |    |  |       | |||||||| || || || || ||||||||||| || ||||||||||| || || || || || ||||||||||||||||| |||||||| |||||||| || |||
--------tacagttttgtttatca-catatttatttcaaatggcttgttttaggctgtgatgttggttgatttgataacttagtctctgataatgctaccttttacagTGGCAAAACCATTGAGCTTGATGATGTTACTTTCCACCAGTGCGTAAATTTGACGAGGTTTAACTCAGAAAAGACCGTCAGTTTTGTGCCACCAGATGGT

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------cagatcgtggtagttttgctcattaatacaatttttttggaacttttttttgtc-atctttgctaaatttgttac------tgattgtgtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
                                                                            ||  |  |   |||  |  ||| |   ||| | ||| | |||     | |     ||||  || | | ||||         ||||| || ||||| |   |||||||||| || || || ||||||||||| ||||||||||| ||||||||  | |||||||| |   | || |||||||||||||| || ||||| || || 
gttgaatgcgcatccacactcttgtgatggcttcgtttaacaatgttgccctcaagtgttttttatttttatttttattttatttactttattttttactctcattctcttgcagcttcgacatatttgggtttgaaaagtgttttacactgtgctcttgtgactcctctttcatgacagTGGGAAAACAATTGAGCTTGATGATGTTACATTCCACCAATGTGTCAATCTCACAAGATTCACTGCTGAGAAGACAGTCAGTTTTGTTCCACCCGATGGA

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------cagatcgtggtagttttgctcat--taatacaatttttttggaacttt----tttttgtcatctttgctaaatttgttactgatt----gtgtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
                                            || |||  |  ||| | |    |  | |  |    ||| |  |||    | ||||  |  |       | |||  | |   |     ||| ||  |||   | ||||||| ||||| || || |||||||| |||||||||||||||||||| ||  | || ||||| ||  | || ||||||||||||||||| ||||| || || 
gttgaatgcacattcctggggcaccctgattttgctatggcttcattgtgcaaagtttccccgagatgcttctttccccttgcagatttgaaatgtttgaaaattggaaggtacttgacattccgtcctgatgtatttccttttacgacagTGGCAAGACAATTGAGCTTGATGACGTCACATTCCACCAGTGTGTGAATCTTACGAGATTCAATGCCGAGAAGACAGTCAGTTTCGTTCCACCGGATGGA

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 7
cagatcgtggtagttttgctcattaatacaatttttttggaacttttttttgt-catctttgctaaatttgttactgattgtgtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
                                          ||||    ||| |||   ||| |  ||| | | ||||      || ||         |||||||| || ||||| || || |||||||| || || ||||| ||||||||||| ||||||||||| || ||||| ||||| || || || || || || 
-------------------------------------gtatgctttaaggtgtacattagtgcaacctttttgattgataaaaatttttc---------agTGGGAAAACGATAGAGCTGGACGATGTCACGTTTCATCAGTGCGTCAACTTAACCAGATTTAACTCCGAGAAGACGGTCAGCTTTGTTCCTCCGGATGGA

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 7
cagatcgtggtagttttgctcattaatacaatttttttggaacttttttttgtcatctttgctaaatttgttactgattgtgtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
                                           | |  |||    | |    ||    ||  ||   ||   |          | | ||||||||| || ||||| || || |||||||| || || ||||| ||||||||||| ||||||||||| || ||||| ||||| || || || || || || 
------------------------------------------gtatgctttaaggtgtacattag---tgcaacctttttgattgataaaaattttgcagTGGGAAAACGATAGAGCTGGACGATGTCACGTTTCATCAGTGCGTCAACTTAACCAGATTTAACTCCGAGAAGACGGTCAGCTTTGTTCCCCCGGATGGA

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|18660565|gb|BM500930.1|BM500930
EST:     GAGGCCCAACTAAAGTCCAGACCAGCAAAGAG                         TGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: GAGGCCCAACTAAAGTCCAGACCAGCAAAGAGgtaaccatat ... tgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|31354959|gb|CD439316.1|CD439316
EST:     AAGATTGGACTTGAAAAAGAGGCCCAACTAAAGTCCAGACCAGCAAAGAG                         TGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATTGGACTTGAAAAAGAGGCCCAACTAAAGTCCAGACCAGCAAAGAGgtaaccatat ... tgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|5525788|gb|AI861681.1|AI861681
EST:     AAGATTGGACTTGAAAAAGAGGCCCAACTAAAGTCCAGACCAGCAAAGAG                         TGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATTGGACTTGAAAAAGAGGCCCAACTAAAGTCCAGACCAGCAAAGAGgtaaccatat ... tgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|91054998|gb|EB165416.1|EB165416
EST:     AAGATTGGACTTGAAAAAGAGGCCCAACTAAAGTCCAGACCAGCAAAGAG                         TGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATTGGACTTGAAAAAGAGGCCCAACTAAAGTCCAGACCAGCAAAGAGgtaaccatat ... tgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|32935086|gb|CF039898.1|CF039898
EST:     AAGATTGGACTTGAAAAAGAGGCCCAACTAAAGTCCAGACCAGCAAAGAG                         TGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
genomic: AAGATTGGACTTGAAAAAGAGGCCCAACTAAAGTCCAGACCAGCAAAGAGgtaaccatat ... tgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT
EST: gi|6021406|gb|AW066334.1|AW066334
EST:     AGAGGCCCAACTAAAGTCCAGACCAGCAAAGAG                         TGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGGGTCAACTT
genomic: AGAGGCCCAACTAAAGTCCAGACCAGCAAAGAGgtaaccatat ... tgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgtcatctttgctaaatttgttactgattgtgtcttctcttgctctacagTGGGAAGACTATAGAACTTGATGATGTCACATTCCACCAGTGTGTCAACTTAACAAGATTTAACTCAGAAAAGACAGTCAGTTTCGTGCCACCTGACGGT
                          tactgat  putative branch site (score: 2)
                                   tgtcttctcttgctct  putative PPT
                 taaatttgtta  TA-rich tract