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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagctcgttagacattaaccctctgccgttgcgaatgttactgccattgcaatatctagaaccatccctctgatcaatttggttgttaatccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTGCTGCGCGTTGGCTTTCTTTAGAGATGGCTTCAGCTGGTGTTGCCCCTTC

Basic information

species Zea mays
transcript GRMZM5G835235_T04
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|13490381|gb|BG517145.1|BG517145
EST:     GGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: GGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|67039601|gb|CO465856.1|CO465856
EST:     GGAAGGAGGATGCCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: GGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|22819758|gb|BU499848.1|BU499848
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|211304795|gb|FL143344.1|FL143344
EST:     AGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: AGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|87156577|gb|DY401366.1|DY401366
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|211304794|gb|FL143343.1|FL143343
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|24773942|gb|CA409196.1|CA409196
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGCTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|211089520|gb|FL366816.1|FL366816
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|26559736|gb|CA831971.1|CA831971
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|32865540|gb|CF005222.1|CF005222
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|211304793|gb|FL143342.1|FL143342
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcaatatctagaaccatccctctgatcaatttggttgttaatccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTGCTGCGCGTTGGCTTTCTTTAGAGATGGCTTCAGCTGGTGTTGCCCCTTC
                                      tgttaat  putative branch site (score: 3)
                                            tccactt  CT-rich tract
     aatatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagctcgttagacattaaccctctgccgttgcgaatgttactgccattgcaatatctagaaccatccctctgatcaatttggttgttaatccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTGCTGCGCGTTGGCTTTCTTTAGAGATGGCTTCAGCTGGTGTTGCCCCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - -tctgccg
- - - - - - - - - - - - - - - - - - - tactgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggttg