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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacaggaagtcgtagtttctacctactggtactgtacgtaaaaaatgtaacacagatcgatacaactcctggtgattgaccctggccttagcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCGGCAGCTGGCCGGCGCCGGCGCCACCGTCGTCGTCTTAACAGCCAGGGAC

Basic information

species Zea mays
transcript GRMZM2G169005_T02
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|211184115|gb|FL126403.1|FL126403
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTATGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|86470243|gb|DY236613.1|DY236613
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|211184114|gb|FL126402.1|FL126402
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|211184116|gb|FL126404.1|FL126404
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|211181714|gb|FL126396.1|FL126396
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|13178344|gb|BG349602.1|BG349602
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|71308191|gb|DR790329.1|DR790329
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|71303157|gb|DR787684.1|DR787684
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|211181715|gb|FL126397.1|FL126397
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|13178343|gb|BG349601.1|BG349601
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|211184113|gb|FL126401.1|FL126401
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|211181712|gb|FL126394.1|FL126394
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCC-
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|93015425|gb|EB640945.1|EB640945
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|211181713|gb|FL126395.1|FL126395
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|211181718|gb|FL126400.1|FL126400
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
EST: gi|78088419|gb|DV516812.1|DV516812
EST:     TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAG                         GATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG
genomic: TTCACGTTCATGGAGGCCGCCGCCATTCCCACCAGTGCCCCGGAAACCAGgtccgtacgt ... agcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtaacacagatcgatacaactcctggtgattgaccctggccttagcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCGGCAGCTGGCCGGCGCCGGCGCCACCGTCGTCGTCTTAACAGCCAGGGAC
                             gattgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacaggaagtcgtagtttctacctactggtactgtacgtaaaaaatgtaacacagatcgatacaactcctggtgattgaccctggccttagcttgacagGATTGCCGTTGTCACCGGCGGCAACAAAGGGATCGGGCTAGAGGTGTGCCGGCAGCTGGCCGGCGCCGGCGCCACCGTCGTCGTCTTAACAGCCAGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - cctactg
- - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - -aacacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgattg