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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactattctttctgcttgatattctattagggtttaaatttctttttcttttatgctgaccaatttttttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG

Basic information

species Zea mays
transcript GRMZM2G011893_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g01410.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------------------gttactattctttctgcttgatattctattagggtttaaatttcttttt-----cttttatgctgacca------atttttttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG
                                                     || |  ||||     |  |  | |    | ||  | |||  | || ||     |||  ||  |||  |      ||| ||||  ||||||||||||    |||||||| || ||||| | |||| ||||||||||||||||||| |||||||||||| | |||||||| ||||||||||||||||||
gtaattattccagtgattttgtgattcccattggctcatgttgttcgacttgatttcacttctagactcaggcaacttgcctgggactaaaaactgttgtttgaaacttccattttgattatttgacattcttttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTAATGAACTGGAATATATAAACGGTGAAGTATGGGCAAATGTCTGGCAG

upper sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G29760.2 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------------------gttactattctttctgcttgatattctattagggtttaaatttctttttcttttatgctgac--caatttttttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG
                                                                          ||  | |   ||    ||||| | |   |||| ||||   || | ||||| |  |   | ||       | |||| || |||  |   |        |||| | ||| | ||| ||||||| | | |||| |||||  ||||||| ||| |||||||||||||||||||||| |    |
gtttgtctgtccaatgaagttctattcctttcctttcaccatttatgtgcaaaacctcattcctaaacctttttgtgtccagctttcaaacttgacaatac-ttagtgtttgctttgcattttcatggaacttaacattgccctctttcctgtagTTGTATCAAAACAAGTTGTCTACTATAAGGGTCATCAAGTACACAATCTCAATGAATTGGAATACATAAATGGTGAAGTCTGGGCAAATGTTTTTATG
















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|211236234|gb|FL280787.1|FL280787
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60352045|gb|DN219018.1|DN219018
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|78179760|gb|DV550133.1|DV550133
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60393994|gb|DN226864.1|DN226864
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|211290372|gb|FL395524.1|FL395524
EST:     AATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: AATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60348982|gb|DN215955.1|DN215955
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|8577165|gb|BE129802.1|BE129802
EST:     GCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: GCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|78122303|gb|DV540687.1|DV540687
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60352117|gb|DN219090.1|DN219090
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|71428221|gb|DR809271.1|DR809271
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60350066|gb|DN217039.1|DN217039
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|211236233|gb|FL280786.1|FL280786
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|211236235|gb|FL280788.1|FL280788
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60357511|gb|DN224484.1|DN224484
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattagggtttaaatttctttttcttttatgctgaccaatttttttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG
                               tgctgac  putative branch site (score: 2)
                                         tttttttcat  putative PPT
          tttaaatttctttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttactattctttctgcttgatattctattagggtttaaatttctttttcttttatgctgaccaatttttttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA