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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattatgtaccagtggattttttttttgtcttgatctgctaaacttgtactgcctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGGCAGTTCACTGCACGAATCTTGGGTGATGATGTCGAGCCTGCAGATGCCA

Basic information

species Zea mays
transcript GRMZM5G846198_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846198_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 16
gtaaaattatgtaccagtgg--------atttt--------ttttttgtcttgatctg---ctaaacttgtactgcctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGGCAGTTCACTGCACGAATCTTGGGTGATGATGTCGAGCCTGCAGATGCCA
|||||||||| |  ||||          |||||        ||| |||||| || ||     |||  || ||   |  ||||| ||||||| | |||||| ||||| ||||||  || |||||||||||||||| |||||||||| |||||||||||||| ||| ||   ||| |  |||   | |
gtaaaattattttgcagtaatagtccatattttgtttcctgtttcttgtctagaactaattttaaggttataaatcgactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGGCAGTTCACAGCACGAATCTTGGGAGATAATCCGGAGTCACCAGGAACTA
















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|32841443|gb|CD981124.1|CD981124
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32840884|gb|CD980565.1|CD980565
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32841205|gb|CD980886.1|CD980886
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32841140|gb|CD980821.1|CD980821
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32838679|gb|CD978357.1|CD978357
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32841510|gb|CD981191.1|CD981191
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32839545|gb|CD979226.1|CD979226
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32841221|gb|CD980902.1|CD980902
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32841148|gb|CD980829.1|CD980829
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|211517235|gb|FL220132.1|FL220132
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|211517236|gb|FL220133.1|FL220133
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|32837859|gb|CD977537.1|CD977537
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|60395365|gb|DN228234.1|DN228234
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
EST: gi|67022576|gb|CO451325.1|CO451325
EST:     AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG
genomic: AGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... ctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accagtggattttttttttgtcttgatctgctaaacttgtactgcctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGGCAGTTCACTGCACGAATCTTGGGTGATGATGTCGAGCCTGCAGATGCCA
                            tgctaaa  putative branch site (score: 2)
                                       tactgcctctttcc  putative PPT
        attttttttttgtctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattatgtaccagtggattttttttttgtcttgatctgctaaacttgtactgcctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGGCAGTTCACTGCACGAATCTTGGGTGATGATGTCGAGCCTGCAGATGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG