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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacagttcatgtatctatgtcctgtaatttcaaaagtgcaacttactcttaagtttacttcttatttctacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG

Basic information

species Zea mays
transcript GRMZM2G113742_T01
intron # 2
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|211108291|gb|FL269574.1|FL269574
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTG
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTG
EST: gi|211108289|gb|FL269572.1|FL269572
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|24773354|gb|CA408608.1|CA408608
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|211222683|gb|FL110211.1|FL110211
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|24961617|gb|CA483617.1|CA483617
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|101389911|gb|EB816886.1|EB816886
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|76909193|gb|DV163265.1|DV163265
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|88757895|gb|DY542036.1|DY542036
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|78073924|gb|DV502358.1|DV502358
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|71309882|gb|DR791225.1|DR791225
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|71426738|gb|DR807788.1|DR807788
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|211108290|gb|FL269573.1|FL269573
EST:     AATGGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTA
genomic: AATGGG-AGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTA
EST: gi|211108297|gb|FL269580.1|FL269580
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAASAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|74235191|gb|DT643105.1|DT643105
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|211109197|gb|FL269582.1|FL269582
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|149007848|gb|EE040277.2|EE040277
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|211108293|gb|FL269576.1|FL269576
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|211108288|gb|FL269571.1|FL269571
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAG
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAG
EST: gi|76932640|gb|DV173098.1|DV173098
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|211222687|gb|FL110215.1|FL110215
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|211222685|gb|FL110213.1|FL110213
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|74240765|gb|DT648679.1|DT648679
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|101386138|gb|EB815112.1|EB815112
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|71318298|gb|DR795913.1|DR795913
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|67026619|gb|CO455368.1|CO455368
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGACGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|101389909|gb|EB816885.1|EB816885
EST:     AAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: AAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|30087488|gb|CB885694.1|CB885694
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
EST: gi|76916798|gb|DV166558.1|DV166558
EST:     CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAG                         AAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA
genomic: CAATGGGAGTGAAGGGCCTCACCCTTTTTCACTTGAAAAGCCATCTTCAGgtacatacag ... tacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatttcaaaagtgcaacttactcttaagtttacttcttatttctacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG
                aacttac  putative branch site (score: 2)
                              tttacttcttatttct  putative PPT
                              tttacttcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacagttcatgtatctatgtcctgtaatttcaaaagtgcaacttactcttaagtttacttcttatttctacttatcagAAATACAGATTGGGAAGACAGTCTGGAAAAGAGTTAACGGAGCAATCAAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG