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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgctcgctggccttctcattattggcatcgtctctgtgtaaatttgggaataatggggttcttggggtctgatgatgtggtgagatgattttgttgttgtgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCAC

Basic information

species Zea mays
transcript GRMZM2G038588_T03
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|211180037|gb|FL171365.1|FL171365
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAV-GNGTACACGTCTGACGAG                         ACTCNAATGGTAATTTATGTCAACACGCACGCCATTCTGGATG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATG
EST: gi|211060219|gb|FL171340.1|FL171340
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211060225|gb|FL171346.1|FL171346
EST:     CGACGGTGGAMCTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATG
EST: gi|211063175|gb|FL171357.1|FL171357
EST:     CGACGGTGGAACTGGACGGBGTGAGCGAGAKCGAGTACACGTCTGACGAG                         ACTCCAATGGTAAT
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAAT
EST: gi|211057223|gb|FL171333.1|FL171333
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGC
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGC
EST: gi|50338324|gb|CO533450.1|CO533450
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211063174|gb|FL171356.1|FL171356
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211060222|gb|FL171343.1|FL171343
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|50338770|gb|CO533896.1|CO533896
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211060214|gb|FL171335.1|FL171335
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|91870592|gb|EB400974.1|EB400974
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211060213|gb|FL171334.1|FL171334
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|149089655|gb|EE178910.2|EE178910
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|31611805|gb|CD568427.1|CD568427
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211063171|gb|FL171353.1|FL171353
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|78122374|gb|DV540758.1|DV540758
EST:     CGACGGGGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAGTGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCGGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|93014407|gb|EB639927.1|EB639927
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACCCGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211063178|gb|FL171360.1|FL171360
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211060216|gb|FL171337.1|FL171337
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211063168|gb|FL171350.1|FL171350
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211063169|gb|FL171351.1|FL171351
EST:     CGACGGTGGAACTGGACGGTGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211060217|gb|FL171338.1|FL171338
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|148972546|gb|EE023508.2|EE023508
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACCCGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211060223|gb|FL171344.1|FL171344
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211060226|gb|FL171347.1|FL171347
EST:     GACGGTGGAACTGGACGGGGTGAGCGAGAGMGTGTTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGT
genomic: GACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGT-ACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGT
EST: gi|71435658|gb|DR816708.1|DR816708
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
EST: gi|211180038|gb|FL171366.1|FL171366
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATG
EST: gi|71323425|gb|DR798363.1|DR798363
EST:     CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAG                         ACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG
genomic: CGACGGTGGAACTGGACGGGGTGAGCGAGAGCGAGTACACGTCTGACGAGgtgagcgctc ... tgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggttcttggggtctgatgatgtggtgagatgattttgttgttgtgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCAC
            gtctgat  putative branch site (score: 4)
                              atgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgctcgctggccttctcattattggcatcgtctctgtgtaaatttgggaataatggggttcttggggtctgatgatgtggtgagatgattttgttgttgtgggttacagACTCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG