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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccttttcatagctattggattgtattgggcacattatattgtatcatttctaagttggttggggaaaaaaaacagtcaccagtaagataggcatcaagacatgggcatagcgacagttctctaaagaatctgtttgcatgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAAGAGCGTCGTCTAGCTCAG

Basic information

species Zea mays
transcript GRMZM2G057412_T04
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057412_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g33590.2 (Oryza sativa), 3'ss of exon 11
gtaaccttttcatagctattggattgtattgggcacattatattgtatcatttctaagttggttggggaaaaaaaacagtcaccagtaagataggcatcaagacatgggcatagcgacagttctctaaagaatctgtttgcatgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAAGAGCGTCGTCTAGCTCAG
                                                 ||   |  || | | |      | | |  | ||    |    | |||||  | || | | | |        |  ||  |||  |         | | | |||||||| |  || |||||||||||||||||||||||||| ||||||||||| ||||||||| |||| || 
-------------------------------------------------atgcttgtgt-gatagacatctagacatggacatttttgttttgggcatgga-acctagacgtgttttttttaatcacaagtgtgatcacctgttcttgcagAAAATCTATAGGTCTGGAGAAGAGAAAGGAAGAGCTCTAAAGTTGAATAAGGAGCGTCGTTTAGCCCAA
















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|74240130|gb|DT648044.1|DT648044
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|93281097|gb|EB673361.1|EB673361
EST:     TTTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCCCCGAAAAG                         AAAATGTTCAGATTTGGAGAAGAGAAAGGAAGAGCTTTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|149102607|gb|EE287965.2|EE287965
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|33467969|gb|CF245018.1|CF245018
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|60336988|gb|DN203961.1|DN203961
EST:     AACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: AACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|76909352|gb|DV163342.1|DV163342
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|211386247|gb|FL227579.1|FL227579
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCCGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|74242217|gb|DT650131.1|DT650131
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCCCCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTTTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|60347261|gb|DN214234.1|DN214234
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|89759386|gb|DY688239.1|DY688239
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCCCCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|86466198|gb|DY232571.1|DY232571
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|211131389|gb|FL432622.1|FL432622
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|60354297|gb|DN221270.1|DN221270
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|89249172|gb|DY620958.1|DY620958
EST:     TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA
EST: gi|211131390|gb|FL432623.1|FL432623
EST:     TTTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAG                         AAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTTTGAAGTTGAATAAA
genomic: TCTTTGACATCAAAATTGATCGTACTGAAAACATGTCAGCCACCGAAAAGgtaacctttt ... atgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaagacatgggcatagcgacagttctctaaagaatctgtttgcatgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAAGAGCGTCGTCTAGCTCAG
                          ctctaaa  putative branch site (score: 3)
                             taaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccttttcatagctattggattgtattgggcacattatattgtatcatttctaagttggttggggaaaaaaaacagtcaccagtaagataggcatcaagacatgggcatagcgacagttctctaaagaatctgtttgcatgcgttcagAAAATGTTCAGATCTGGAGAAGAGAAAGGAAGAGCTCTGAAGTTGAATAAAGAGCGTCGTCTAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA