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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatctcaatctccacatgcgattcacactcctgtcgtgagcttaatccggacaagccgattcttttccttggatctaactcctccccaacatttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA

Basic information

species Zea mays
transcript GRMZM2G136803_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 3'ss of exon 22
gaatctcaatctccacatgcgattcacac---tcctgtcgtgagctt---aatccggac---aagccgatt-cttttccttggatctaactcctccccaacatttttc--agGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA
            ||| ||   |||  | |    ||||| || |  ||   || ||  |    |||  | ||  ||||||||| |||||||| ||||||   |||| |   |||  | || ||||||||||| || ||| || |||| ||||||||||| |||||||||||||| || |||||||| ||||||||||| || || || |||  
------------ccatataaaatttgcgcattccctgttgtaaatttggcaacccataattgaaggtgtttgtttttccttgcatctaacttctcccctctatttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAACCATCAAGGAACTTGTCACAAGTAGTGGGAGGTCATTTCCTGGTAAGGT

upper sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 21
-----gaatctcaatctccacatgcgattcacactcctgtcgtgagcttaatccggacaa-gccgattcttttccttggatctaactcctccccaacatttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA
       || | ||| |     ||   |||      |     |||  | | | | ||        |   |  ||  || ||    ||||| |       |  |||||||| || ||||||||||||||| ||||||| ||||| ||  |  |  ||||||||| ||| || ||     |||||||  |  | |  ||   |     
atagatgatttaaatttttg--tgtttttcttgtcgcaaaattgatttcatttctgattgtattaaagttcctctctgcatgctgctcctacttg----tactcagGTGTGCATGTGACATTGGAGTCCTTGCTGAAGGACAAAGAACTTAAAACAACCATCAGGGAGCTTGTACACTGCAGTGGACGAGCGTATCCTCTAGTTGG
















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|6022364|gb|AW067292.1|AW067292
EST:     AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC                         GTGTCCACGTGACATTGGAGTCCCTGCTGANCGACAAGGACATCCAGGCAN
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST: gi|16927586|gb|BM080655.1|BM080655
EST:     AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC                         GTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST: gi|78120826|gb|DV539210.1|DV539210
EST:     AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC                         GTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST: gi|32867796|gb|CF007478.1|CF007478
EST:     AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC                         GTGTCCACGTGACATTGGAGTCCCTGCTGAACGATAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST: gi|60394528|gb|DN227398.1|DN227398
EST:     AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC                         GTGTCCACGTGACATTGGAGTCCCTACTGAACGACAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST: gi|76015306|gb|DT942476.1|DT942476
EST:     AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC                         GTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA
EST: gi|32944133|gb|CF048952.1|CF048952
EST:     AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC                         GTGTCCACGTGACATTGGAGTCCCTGCTGAACGATAAGGACATCCAGGCAA
genomic: AGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaat ... catttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccggacaagccgattcttttccttggatctaactcctccccaacatttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA
                            atctaac  putative branch site (score: 2)
                                             catttttc  putative PPT
                                           aacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatctcaatctccacatgcgattcacactcctgtcgtgagcttaatccggacaagccgattcttttccttggatctaactcctccccaacatttttcagGTGTCCACGTGACATTGGAGTCCCTGCTGAACGACAAGGACATCCAGGCAACCATCAAGGACCTGGTCACAAGCAGTGGGAGGTCCTTCCCCGGAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - -catgcga
- - - - - - - - - - - - - -actcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcc