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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgaaaaattatcacattgtcatcagatcagatgtcaagaccatctggataattctagaaagaagcaatttcaattacattgttctggtgaccttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 11
--gtagtga-aaaattatcacatt--gtcatcagatcagatgtcaagaccatctggat--aattctagaaagaagcaatttcaatta--cattgttctggtgaccttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG
  |  |  | |||||| ||||  |    | |||   ||  | || |||  ||   |     |||||     ||   || || ||||     || |     || |||| |||||||||||||||||| |||| ||||||||||||||| |||||||||||||| ||||| ||| |||| ||||||||||| ||||||||||| ||||||
gtgctgcaataaaattgtcactcttgaccttcatcccaactatctagataatagtggccggattctcctttgatagaaattaaattgtttgttatgtgaatgcccttaacagCTTAGAGAATCAATGGACAAAAGCACTGCTGTATTTGACAAAGAAAAGGCTCAAGAACGTCTATCAAAGTTATCTGGTGGTGTTGCTGTCCTCAAG
















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|18450678|gb|BM428956.1|BM428956
EST:     TCCTAGATGGTGGAGGTGACAACCAGCAGATAGATGAGAGGTGCCACCAG                         CTTAGAGATATCAATTGACACAAGC-CATGCTGTATTCGACAAAGAAAAGG
genomic: TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAGgtagtgaaaa ... accttgacagCTTAGAGA-ATCAATTGACACAAGCAC-TGCTGTATTCGACAAAGAAAAGG
EST: gi|67028320|gb|CO457069.1|CO457069
EST:     TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAG                         CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
genomic: TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAGgtagtgaaaa ... accttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
EST: gi|87152753|gb|DY397542.1|DY397542
EST:     TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAG                         CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
genomic: TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAGgtagtgaaaa ... accttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
EST: gi|19822484|gb|BQ048508.1|BQ048508
EST:     TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAG                         CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
genomic: TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAGgtagtgaaaa ... accttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
EST: gi|76911014|gb|DV164129.1|DV164129
EST:     CAAACAGCAGATAGATGAGAGGTGCCAACAG                         CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
genomic: CAAACAGCAGATAGATGAGAGGTGCCAACAGgtagtgaaaa ... accttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
EST: gi|211181730|gb|FL012621.1|FL012621
EST:     TCCTAGATGGTGGAGGTGACAAACAGCAGATAGAGGAGAGGTGCCAACAG                         CTTAGAGACTCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
genomic: TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAGgtagtgaaaa ... accttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
EST: gi|22489691|gb|BU049614.1|BU049614
EST:     TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCACCAG                         CTTAGAGAATCAATTGACCCAAGCCCTGCTGTATTCGACAAAGAAAAGGCC
genomic: TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAGgtagtgaaaa ... accttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
EST: gi|87153562|gb|DY398351.1|DY398351
EST:     TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAG                         CTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC
genomic: TCCTAGATGGTGGAGGTGACAAACAGCAGATAGATGAGAGGTGCCAACAGgtagtgaaaa ... accttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggataattctagaaagaagcaatttcaattacattgttctggtgaccttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG
                     aatttcaattacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgaaaaattatcacattgtcatcagatcagatgtcaagaccatctggataattctagaaagaagcaatttcaattacattgttctggtgaccttgacagCTTAGAGAATCAATTGACACAAGCACTGCTGTATTCGACAAAGAAAAGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG