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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatctctgttctttattctatattcattgtcatattttccctttaactaattatagtttgagttacgccagtaaccctcatttctgtttcctttatgatcgactattcttgtcatttttagAGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGACCTTAATAATTCTGGGAG

Basic information

species Zea mays
transcript GRMZM2G036872_T01
intron # 3
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|89247360|gb|DY619146.1|DY619146
EST:     GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCT                         AGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGAC
genomic: GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCTgttagcatct ... tcatttttagAGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGAC
EST: gi|211508932|gb|FL160996.1|FL160996
EST:     GCTGGTTCATCCTCACACGAACATCACTGGTCTTCTTCAAGAGTGATCCT                         AGTACGTTACCACA
genomic: GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCTgttagcatct ... tcatttttagAGTACGTTACCACA
EST: gi|149074588|gb|EE162991.2|EE162991
EST:     GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCT                         AGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGAC
genomic: GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCTgttagcatct ... tcatttttagAGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGAC
EST: gi|211508931|gb|FL160995.1|FL160995
EST:     CTGGTTCATCCTCACACGAACATCACTGGTTTTTCTTCAAGAGTGATCCT                         AGTACGTTACCACAGAGAAGTGAAGTG
genomic: CTGGTTCATCCTCACACGAACATCACTGGTTTT-CTTCAAGAGTGATCCTgttagcatct ... tcatttttagAGTACGTTACCACAGAGAAGTGAAGTG
EST: gi|149074587|gb|EE162990.2|EE162990
EST:     CACTGGTTTTCTTCAAGAGTGATCCT                         AGTACGTTACCACAGAGGAAGTGAAGTGAACCTTACATTGGGAGGAATTGA
genomic: CACTGGTTTTCTTCAAGAGTGATCCTgttagcatct ... tcatttttagAGTACGTTACCACAGA-GAAGTGAAGTGAACCTTACATTGGGAGGAATTGA
EST: gi|211508933|gb|FL160997.1|FL160997
EST:     GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCT                         AGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGAC
genomic: GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCTgttagcatct ... tcatttttagAGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGAC
EST: gi|211508930|gb|FL160994.1|FL160994
EST:     GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCT                         AGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGAC
genomic: GCTGGTTCATCCTCACACGAACATCACTGGTTTTCTTCAAGAGTGATCCTgttagcatct ... tcatttttagAGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccagtaaccctcatttctgtttcctttatgatcgactattcttgtcatttttagAGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGACCTTAATAATTCTGGGAG
  cagtaac  putative branch site (score: 2)
                                       ttcttgtcattttt  putative PPT
                                             tcattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatctctgttctttattctatattcattgtcatattttccctttaactaattatagtttgagttacgccagtaaccctcatttctgtttcctttatgatcgactattcttgtcatttttagAGTACGTTACCACAGAGAAGTGAAGTGAACCTTACATTGGGAGGAATTGACCTTAATAATTCTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA