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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTTACAACCCACCATTGGATGGTCCGCATATATAAACTGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaacgacctgctgtatagttataatgtattgttctttttgtgtccatcctaacacattatatgccgttttgtacctgcag

Basic information

species Zea mays
transcript GRMZM2G060611_T02
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060611_T03 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os05g44360.2 (Oryza sativa), 5'ss of exon 16
GTATTTACAACCCACCATTGGATGGTCCGCATATATAAACTGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaacgacctgctgtatagttataatg-tattgttctttttgtgtccatcctaacacattatatgccgttttg------tacctgcag
|| || ||||||||||| ||||||||||| ||||||||||||||||| || ||||| |||||||| |||||| |||||||||||||  | |||||||   | |  |  |  ||  | | |    |||| |  |   | ||    |   ||||||||  |     ||| |      || | ||||
GTTTTCACAACCCACCACTGGATGGTCCGTATATATAAACTGAAACCTCAAAAGAATAGGGTTCGGGGCAAGTTGAAGAAGTTGAAATCTgtaagtctggcaaattttta-attttcacacccctattctgataactttgaa-gtttgaacacatttaaccttttttcgcttgcttatccgcag
















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|211090145|gb|FL283407.1|FL283407
EST:     TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|211411800|gb|FL441053.1|FL441053
EST:     TGAAACCCCAGAAGAACASVRNWCBAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCC-AAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCA
EST: gi|4804481|gb|AI665351.2|AI665351
EST:     TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|5686744|gb|AI939837.1|AI939837
EST:     GAAACCCCAGAAGAACAGGGTTCGAGGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: GAAACCCCAGAAGAACAGGGTTCGA-GGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|5686787|gb|AI939880.1|AI939880
EST:     TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACCTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|4827671|gb|AI668363.1|AI668363
EST:     TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|78025639|gb|DV494026.1|DV494026
EST:     TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|4826194|gb|AI667822.1|AI667822
EST:     AAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGANNAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: AAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGA--AGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|5343076|gb|AI795486.1|AI795486
EST:     TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|166689566|gb|EG296454.1|EG296454
EST:     TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTTCCACACTTGCGGCCGGGCGAAAGAACCCGTGGCAA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
EST: gi|76911616|gb|DV164349.1|DV164349
EST:     TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCC                         AGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA
genomic: TGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaa ... gtacctgcagAGTGCCAAAACTAGTCCCACACTTGCGGCAGGGCGAAAGAACCCGTGGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTTACAACCCACCATTGGATGGTCCGCATATATAAACTGAAACCCCAGAAGAACAGGGTTCGAGGCAAGCTGAAGAAGTTGAAGGCCgtaagtcgaacgacctgctgtatagttataatgtattgttctttttgtgtccatcctaacacattatatgccgttttgtacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG