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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcctttcattgtggccgtactagattcatctcaaatctaggctacagtggatattgctaatttgtaatttctcaccatgaatattatttatgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGGTATAATTAGTGGGGACTCGCCTAGGCACAGCTCACCAGCATCGAAGTTA

Basic information

species Zea mays
transcript GRMZM2G142693_T02
intron # 1
splice site 3'
intron type U2

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|148949779|gb|EC895262.2|EC895262
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263297|gb|FL247912.1|FL247912
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211260869|gb|FL247908.1|FL247908
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211265737|gb|FL247925.1|FL247925
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263296|gb|FL247911.1|FL247911
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263308|gb|FL247923.1|FL247923
EST:     GGGTGGAAGTGAGTGCCGGGTGATCCATCCGGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: -GGTGG-AGTGAGTGCC-GGTGATCCATCC-GGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263294|gb|FL247909.1|FL247909
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263305|gb|FL247920.1|FL247920
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263302|gb|FL247917.1|FL247917
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263295|gb|FL247910.1|FL247910
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|71438786|gb|DR819836.1|DR819836
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263300|gb|FL247915.1|FL247915
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263303|gb|FL247918.1|FL247918
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263306|gb|FL247921.1|FL247921
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263307|gb|FL247922.1|FL247922
EST:     -CCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|67033577|gb|CO462326.1|CO462326
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211265736|gb|FL247924.1|FL247924
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263299|gb|FL247914.1|FL247914
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTT-CACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263298|gb|FL247913.1|FL247913
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263301|gb|FL247916.1|FL247916
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211265738|gb|FL247926.1|FL247926
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
EST: gi|211263304|gb|FL247919.1|FL247919
EST:     TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCG                         GCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG
genomic: TGCTGGTGGAGTGAGTGCCGGTGATCCATCCGGAGTTGGATTTGTCCTCGgtaaggagat ... atgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtggatattgctaatttgtaatttctcaccatgaatattatttatgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGGTATAATTAGTGGGGACTCGCCTAGGCACAGCTCACCAGCATCGAAGTTA
                        ttctcac  putative branch site (score: 2)
                                              tgtctcc  putative PPT
                                atgaatattatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcctttcattgtggccgtactagattcatctcaaatctaggctacagtggatattgctaatttgtaatttctcaccatgaatattatttatgtctccagGCAAGGAGGTTTTGCACCATACAAGATCGTCAAAATTGCCGAAATGGGAGGTATAATTAGTGGGGACTCGCCTAGGCACAGCTCACCAGCATCGAAGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
tgccttt
- - - - - - - - - - - - - - - - - - - - -gctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctaa