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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttccttttattttcatatatattgtatccctttgcattgtctccgattacctcttgcatcagatggcagtgctatattctcttgaaaatcagaagtgatgtcaatactcatattttttcaatcttttattttttattgtcactcacaattttttttgtttgaatag

Basic information

species Zea mays
transcript GRMZM2G124886_T01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 22
CAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttccttttattttcatatatattgtatccctttgc---attgtctccgattacctcttgcatcagatggca-gtgctatattctcttgaaaatcagaagtgatgtcaatactcatattttttcaatcttttattttttattgtcactcacaattttttttgtttgaatag
| ||||| || || ||  |||| ||||| || |||||||||||||| |||||||||||||| |||||||| ||||||||||||  |||||| || |||||||       |  ||| |     || | | | | | | ||||    | | |  ||  ||  ||||| || || |||| |   ||  |  |   |||     |     |                                                                      
CCAAAGCGGCAGAATCATTGGCAGATCCCAACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTTGCGCCCAAAAGgt-------ctgtttgtaaaagtaaaaactatgttcttttgtgaaagttttacctgttctctcttcca-cacatgggacaagccgtcatggtttgctttcctcttctc---------------------------------------------------------------------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 5'ss of exon 13
CAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttccttttattttcatatatattgtatccctttgcattgtctccgattacctcttgcatcagatggcagtgctatattctcttgaaaatcagaagtgatgtcaatactcatattttttcaatcttttattttttattgtcactcacaattttttttgtttgaatag
| |||||||| || ||  |||| |||||| | |||||||||||||| |||||||||||||| |||||||| ||||||||||||  ||| || || |||||||||  |||| |   |      || | | | | | | ||||       |    |||||                ||| || | |||  |     ||  ||   |  |||||   |    ||  |    ||                                           
CCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGCCCAAAAGgtat--gttcgtaaaa-----gtaaaaactatgttcttttgtgaaagtt----ttacc----------------agttctctcttccat---gcatgggacaagtcgtcaaggtttgctttcctcttctc-------------------------------------------
















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|32794634|gb|CD946870.1|CD946870
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCCCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|211291669|gb|FL235609.1|FL235609
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCCCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19822105|gb|BQ048129.1|BQ048129
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19822050|gb|BQ048074.1|BQ048074
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19821973|gb|BQ047982.1|BQ047982
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|26455841|gb|CA827424.1|CA827424
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19821970|gb|BQ047979.1|BQ047979
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|5847331|gb|AW000410.1|AW000410
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGGTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|111145650|gb|EE257974.1|EE257974
EST:     AGACTGGCAGATTNGCTCTGAATGTAAAAACCTGCTGTTGCCCCGAAAAG                         GGTTATCTATCC
genomic: AGACTGGCAGATT-GCTCTGAATGTAGAAGC-TGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCC
EST: gi|19822070|gb|BQ048094.1|BQ048094
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19822158|gb|BQ048182.1|BQ048182
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|67014399|gb|CO443148.1|CO443148
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|26456008|gb|CA827591.1|CA827591
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttccttttattttcatatatattgtatccctttgcattgtctccgattacctcttgcatcagatggcagtgctatattctcttgaaaatcagaagtgatgtcaatactcatattttttcaatcttttattttttattgtcactcacaattttttttgtttgaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT