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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaacaatcatgggcagtaagtttacaagactatttcttttttcattgtccttaaaatctttcatgcttccag

Basic information

species Zea mays
transcript GRMZM5G852877_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G852877_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g74640.1 (Oryza sativa), 5'ss of exon 4
TGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaacaat----------catgggcagtaagtttacaagactatttcttttttcattgtccttaaaatctttcatgcttccag
||||||||||||||| || ||||||||||||||||| || | |||| ||||||||   |||||||||||||| ||||| || ||||| ||||||||||||||| ||   |||||          |||| ||||||| || | || |  |||  | ||  |   | |||  ||||||| |||  || |||
TGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAGAGGCACTATTCTGGAGCCCTCAATGCGTATGCTACCATAATCAGACAGgttgctgctacaattcatggtgatcatgagcagtaaattaaaaaaaaaattcatattccccacggcctgtaaatctt-catattttcag
















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

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAGAGGAGTTATTCTGGAGCCCTTAATGCATACGCTACAATAATCAGACAGgttactttaacaatcatgggcagtaagtttacaagactatttcttttttcattgtccttaaaatctttcatgcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG