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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccagccattctgaagtctgaaccacacacatacgttatacgtatacatggaaaaatgatgggataactgaacctgtcttgttcgacccacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCTTCTCCAAGAAGGGGATGAAGGGCAAGTCCGTGAGCGGGATGAACTACTA

Basic information

species Zea mays
transcript GRMZM2G125850_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|211236186|gb|FL162466.1|FL162466
EST:     CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTG                         GGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
genomic: CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTGgtgagtgaca ... cacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
EST: gi|27753886|gb|BM378078.1|BM378078
EST:     CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTG                         GGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
genomic: CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTGgtgagtgaca ... cacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
EST: gi|24934556|gb|CA452774.1|CA452774
EST:     TGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTG                         GGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
genomic: CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTGgtgagtgaca ... cacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
EST: gi|50335221|gb|CO530347.1|CO530347
EST:     CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTG                         GGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
genomic: CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTGgtgagtgaca ... cacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
EST: gi|93282359|gb|EB674623.1|EB674623
EST:     GCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTG                         GGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCCTCT
genomic: GCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTGgtgagtgaca ... cacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
EST: gi|71770113|gb|DR968050.1|DR968050
EST:     CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTG                         GGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
genomic: CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTGgtgagtgaca ... cacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
EST: gi|89249586|gb|DY621372.1|DY621372
EST:     CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTG                         GGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT
genomic: CGGTGGGTGCGCGCTCGCCGCCGTCACCGAGCTCAACTTCAACATGGTTGgtgagtgaca ... cacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatggaaaaatgatgggataactgaacctgtcttgttcgacccacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCTTCTCCAAGAAGGGGATGAAGGGCAAGTCCGTGAGCGGGATGAACTACTA
                  ggataac  putative branch site (score: 3)
        aaaaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccagccattctgaagtctgaaccacacacatacgttatacgtatacatggaaaaatgatgggataactgaacctgtcttgttcgacccacgctgtagGGTTCATGGGGGCAATGATCTCGAACCTGGCGTTCGTCGTCCGGACCATCTTCTCCAAGAAGGGGATGAAGGGCAAGTCCGTGAGCGGGATGAACTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG