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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactcctttgtagtaccctgtaaaattttcatcttgttttggtagtgggtcaaattttctgcgtaactaatcctggcattcgtgtctttatttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA

Basic information

species Zea mays
transcript GRMZM2G110714_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 9
tactcctttgtagtaccctgtaaaattttcatcttgttttggtagtgggtcaaattttctgcgtaactaatcctggcattcgtgtctttatttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA
      ||  ||     ||  |  | |    ||||       | || | | |||      | |   ||||     |  || | || | ||||    | ||||||| |||||| | |||||||| ||||||||||| |||||| | ||||| ||| | || || || |  || |||||||||||||| |||||||| ||||
-gtaagttcttaaccagctcaattactcctctcttaaacaaattgtagttaaaaaa----gagagtctaagttcag-gtttgggtttgtatt----atagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 8
----tactcctttgtagtaccctgtaaaattttcatcttgttttggtagtgggtcaaattttctgcgtaactaatcctggcattcgtgtctttatttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA
     | |   ||| | |  |   |||    |    | ||  ||  |    |   |      |        | ||  |   ||   | |   | ||  |  |||||||| |||||| ||||||||||| |||||||||| |||||  | ||||| ||| ||||||| |||| |||||| ||||| || ||||||||||| ||||
tcataatttgcttgcatttacaaataattcctgagccctgcatttctcactgtgaagg----caataatggtgatggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA
















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|211502934|gb|FL212597.1|FL212597
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|211505276|gb|FL212599.1|FL212599
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|211505277|gb|FL212600.1|FL212600
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|26457670|gb|CA829253.1|CA829253
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATATTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|211502933|gb|FL212596.1|FL212596
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCMGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|60353908|gb|DN220881.1|DN220881
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtcaaattttctgcgtaactaatcctggcattcgtgtctttatttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA
                   aactaat  putative branch site (score: 2)
                                       tctttattt  putative PPT
                                         tttatttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactcctttgtagtaccctgtaaaattttcatcttgttttggtagtgggtcaaattttctgcgtaactaatcctggcattcgtgtctttatttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA