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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagcttcttctcaattgaaacaaatatatccgctcccggcagttccaaagaaacttcttttggggtgctaagacatgtttttttaaccatcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGCTGTACATCCTGATGAAGATTTTGCACACCTGTCATTTTGTATACACTGC

Basic information

species Zea mays
transcript GRMZM2G000393_T01
intron # 11
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|32928477|gb|CF033289.1|CF033289
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|71435122|gb|DR816172.1|DR816172
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|60338589|gb|DN205562.1|DN205562
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|71436236|gb|DR817286.1|DR817286
EST:     TGCAACTTACGTGGATGATGCCCGGTTGTGCTGCAGCAGTTCCAGCCAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|50323552|gb|CO518678.1|CO518678
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|166453596|gb|EG280202.1|EG280202
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGC
EST: gi|4775973|gb|AI664976.1|AI664976
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|78021331|gb|DV489718.1|DV489718
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|32846895|gb|CD986576.1|CD986576
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAGGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|60346760|gb|DN213733.1|DN213733
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|71426993|gb|DR808043.1|DR808043
EST:     TGCAACTTACGTGGATGATGCCCGGTTGTGCTGCAGCAGTTCCAGCCAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|32929367|gb|CF034179.1|CF034179
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|211130918|gb|FL136656.1|FL136656
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|4621425|gb|AI612258.1|AI612258
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTAC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|50334717|gb|CO529843.1|CO529843
EST:     TGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|61119808|gb|DN560769.1|DN560769
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|60344825|gb|DN211798.1|DN211798
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|149005473|gb|EE040028.2|EE040028
EST:     TGCAACTTACGTGGATGATGCCCGGTTGTGCTGCAGCAGTTCCAGCCAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|71772159|gb|DR970096.1|DR970096
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGCCAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|149096404|gb|EE182138.2|EE182138
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|166598258|gb|EG127937.1|EG127937
EST:     GGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: GGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|110200892|gb|EC882789.1|EC882789
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATTTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|24765385|gb|CA400544.1|CA400544
EST:     TGCAACTTACGTGGATGATGCCCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|45847888|gb|CN071831.1|CN071831
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGTAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|26557287|gb|CA829522.1|CA829522
EST:     TGCAACTTACGTGGATGATGCCCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|21828587|gb|BQ703271.1|BQ703271
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|78093004|gb|DV521378.1|DV521378
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|211130920|gb|FL136658.1|FL136658
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTT
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTT
EST: gi|60346466|gb|DN213439.1|DN213439
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|148940752|gb|EC885572.2|EC885572
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|15082759|gb|BI389443.1|BI389443
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|113703856|gb|EE681360.1|EE681360
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
EST: gi|5124017|gb|AI745858.1|AI745858
EST:     TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAG                         AGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC
genomic: TGCAACTTACGTGGATGATGACCGGTTGTGCTGCAGCAGTTCCAGACAAGgtacagcttc ... tcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaagaaacttcttttggggtgctaagacatgtttttttaaccatcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGCTGTACATCCTGATGAAGATTTTGCACACCTGTCATTTTGTATACACTGC
                                    ttttaac  putative branch site (score: 2)
                                             tcgtttcc  putative PPT
                            acatgtttttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagcttcttctcaattgaaacaaatatatccgctcccggcagttccaaagaaacttcttttggggtgctaagacatgtttttttaaccatcgtttccagAGAAAATCTGTTCCAATGCTTGAGCGGAAGGCGTGGCTGCTGGCCTGTTGCTGTACATCCTGATGAAGATTTTGCACACCTGTCATTTTGTATACACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA