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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactttaacaatcatgggcagtaagtttacaagactatttcttttttcattgtccttaaaatctttcatgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG

Basic information

species Zea mays
transcript GRMZM5G852877_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g74640.1 (Oryza sativa), 3'ss of exon 4
---------gttactt-taacaatcatgggcagtaagtttacaagactatttcttttttcattgtccttaaaatctttcatgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG
            | |  |    |||||| ||||||| || | || |  |||  | ||  |   | |||  ||||||| |||  || |||||||||||||||||||||||||||||||| ||||||||  | ||||||||||| |||||||| ||| |||||||||||||||| || ||  ||||||||
gttgctgctacaattcatggtgatcatgagcagtaaattaaaaaaaaaattcatattccccacggcctgtaaatctt-catattttcagGAAGGTATTGGAGCTTTGTGGACTGGCCTCGGTCCAAACATAGCACGCAATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAG

upper sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------gttactttaacaa--tcatgggcagtaagttt----acaagactatttcttttttcattgtcc--------ttaaaatctttcatgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG
                                                                    || ||| |   |  |||    || | |  |     |      | |||   ||| ||   |||        | |||   | |  || ||  |||||||  |   |   ||||||||||| ||||||||||||||||| || || || || || || ||||| ||||||||||| ||||| ||  |||| |||
gtctgagccccatgatctatagctttaataaatctgagctttctaatttacactcatgatacagagcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtg-ttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG
















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|89762468|gb|DY690033.1|DY690033
EST:     AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
EST: gi|93017381|gb|EB642901.1|EB642901
EST:     GAGCCCTTAATGCATACGCTACAATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: GAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
EST: gi|78084604|gb|DV512997.1|DV512997
EST:     AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
EST: gi|84980856|gb|DW531205.1|DW531205
EST:     AGAGGAGTTATTCTGGAGCCCTTAATGCATATGCTACAATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
EST: gi|6527113|gb|AW216323.1|AW216323
EST:     CAATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: CAATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
EST: gi|93017382|gb|EB642902.1|EB642902
EST:     AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
EST: gi|60354253|gb|DN221226.1|DN221226
EST:     AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
EST: gi|60401298|gb|DN234105.1|DN234105
EST:     AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: AGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
EST: gi|101399785|gb|EB821739.1|EB821739
EST:     AATAATCAGACAG                         GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT
genomic: AATAATCAGACAGgttactttaa ... atgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttacaagactatttcttttttcattgtccttaaaatctttcatgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG
                                       tctttcatgcttcc  CT-rich tract
             tatttcttttttcatt  TA-rich tract