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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttcttgatgcacccaaatgattttttttttgttcctctacattcatgtgccaggatttcgaacagttcttgtagctaatatcttcatttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATG

Basic information

species Zea mays
transcript GRMZM2G073415_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048150_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 1
tttttcttgatgcacccaaatgattttttttttgttcctctacattcatgtgccaggatttc----gaacagttcttgta-gctaatatcttcatttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATG
   ||||   | ||||||||||| || |  ||   |||| | ||| ||||||| |   | ||     || |||  || |  ||| |    |  ||     || ||||||| ||||||||||||||||||||||||||||||||||||||||| |||||
---ttctgttttcacccaaatgagttatacttc--tcctgtccatgcatgtgctaaattatcttcaaaatagtagttctgtgcttaaccttgtatgattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG
















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|76291081|gb|DV030649.1|DV030649
EST:     CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
EST: gi|211358955|gb|FL199138.1|FL199138
EST:     CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
EST: gi|211358956|gb|FL199139.1|FL199139
EST:     CCGTCAAGTCGCTGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
EST: gi|91055827|gb|EB166245.1|EB166245
EST:     CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
EST: gi|148971483|gb|EE022178.2|EE022178
EST:     CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
EST: gi|211358959|gb|FL199142.1|FL199142
EST:     CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
EST: gi|211358960|gb|FL199143.1|FL199143
EST:     CCGTCAAGTCGCTGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGG
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGG-
EST: gi|211358954|gb|FL199137.1|FL199137
EST:     CCGTCAAGTCGCTGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
EST: gi|33468142|gb|CF245191.1|CF245191
EST:     CCGCCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
EST: gi|37426041|gb|CF650771.1|CF650771
EST:     CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAG                         GCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA
genomic: CCGTCAAGTCGCCGCCGCGACCCAGCTCGCCTGCCACGTCCACTCGCAAGgtccgaatcc ... ttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtgccaggatttcgaacagttcttgtagctaatatcttcatttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATG
                              agctaat  putative branch site (score: 3)
                                      tcttcatttc  CT-rich tract
                                 taatatcttcatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttcttgatgcacccaaatgattttttttttgttcctctacattcatgtgccaggatttcgaacagttcttgtagctaatatcttcatttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA