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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactgcttttacgaacagcttaattcagtatcaacagttaaggcgaaaaggaacttttattctgcttaggactttcagccctctgtgttttgggt...

Basic information

species Zea mays
transcript GRMZM2G408242_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 5'ss of exon 6
GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactgcttttacgaacagcttaattcagtatcaacagttaaggcgaaaaggaacttt-tattctgcttaggac---tttcag---ccctctgtgttttgggt
||| ||||||||||||||||||||||| ||||||||||||||||||||    ||  | |||  ||||  ||   |   | | | | || ||| |      ||  ||| | || |||  |  |    ||| ||   |  ||||   |||||  
GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgta----ctcttcttat-aacaatttgcatttttgt-atctgtgaagtctgttttgagttttgttttatgcagaaaagctgttttagatgctttctggcatttggt-
















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|211115727|gb|FL229698.1|FL229698
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCGTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTAGTC-TCATATACCCT
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCC-TGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTA-TCCTCATATACCCT
EST: gi|211116530|gb|FL229719.1|FL229719
EST:     GTTNGT-GCAGGATGCTGGCATAACAGACCTGACACATTTTGCCTG                         GGGCCTTGTTTATGATACATACCAGATGGACC
genomic: GTT-GTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACC
EST: gi|50333682|gb|CO528808.1|CO528808
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|211117330|gb|FL229739.1|FL229739
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|22818772|gb|BU498862.1|BU498862
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|5325108|gb|AI783299.1|AI783299
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGNTAATGATACATACAAGATGGACCTTATCCTCATATACCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCC
EST: gi|148937775|gb|EC881986.2|EC881986
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|6020447|gb|AW065375.1|AW065375
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGNTAATGATACATACAAGATGGACCTTATCCTCATATACCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCC
EST: gi|149084617|gb|EE174095.2|EE174095
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|148990759|gb|EE032170.2|EE032170
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|26456727|gb|CA828310.1|CA828310
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|74237502|gb|DT645416.1|DT645416
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|22521612|gb|BU080423.1|BU080423
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactgcttttacgaacagcttaattcagtatcaacagttaaggcgaaaaggaacttttattctgcttaggactttcagccctctgtgttttgggt

- - - - AGGATG
- - - - -  ATGCTG