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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattctgctgctgaagtacccacactgtgttgcatttagcaagttacaaaacaacaatcaattttgcaaagacatgattaccggttcttcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTGGGGACTTCTACAACGCCTATTTTCAG

Basic information

species Zea mays
transcript GRMZM2G030299_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030299_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g02640.1 (Oryza sativa), 3'ss of exon 7
----aatattctgctgctgaagtacccacactgtgttgcatttagcaagttacaaaacaacaatcaattttgcaaagacatgattaccggttcttcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTGGGGACTTCTACAACGCCTATTTTCAG
     || ||    |||     |  |     ||| ||   | | |||  | |  |  ||  |  |||||  |  || | |   |||  |  | || |||||||||||| |||||||| || |||||||| ||||| ||||| ||||||||||| ||||| ||||| | | |||||||| ||
tgttcatgttgatatgcctggattactg-gttgtcttatctatggcacatcatgac-cagtagacaattc-gttaacagaaacttattg-ctgtttaactgcagATGGCCACAACGAAGCGGAGTTTGGTATGTCATGGTGCGCTGGATTTGGGGGGGAATTCTATAGCTCCTATTTTGAG
















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|60337252|gb|DN204225.1|DN204225
EST:     AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACT                         ATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
genomic: AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACTgtaagtaaaa ... tcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
EST: gi|76283912|gb|DV023480.1|DV023480
EST:     AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACT                         ATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
genomic: AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACTgtaagtaaaa ... tcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
EST: gi|149108778|gb|EE189830.2|EE189830
EST:     AAGCTTTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACT                         ATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
genomic: AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACTgtaagtaaaa ... tcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
EST: gi|60348350|gb|DN215323.1|DN215323
EST:     AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACT                         ATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
genomic: AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACTgtaagtaaaa ... tcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
EST: gi|76288116|gb|DV027684.1|DV027684
EST:     AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACT                         ATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
genomic: AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACTgtaagtaaaa ... tcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
EST: gi|78544199|gb|DV621697.1|DV621697
EST:     AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACT                         ATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
genomic: AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACTgtaagtaaaa ... tcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
EST: gi|211523349|gb|FL468083.1|FL468083
EST:     AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACT                         ATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
genomic: AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACTgtaagtaaaa ... tcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
EST: gi|76283911|gb|DV023479.1|DV023479
EST:     AAGCTTTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACT                         ATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG
genomic: AAGCTCTGATAGCAATGGGGATCCTGTAATATTGGATCCTGCTTGCTACTgtaagtaaaa ... tcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacaaaacaacaatcaattttgcaaagacatgattaccggttcttcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTGGGGACTTCTACAACGCCTATTTTCAG
                                         ttcttc  CT-rich tract
            aatcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattctgctgctgaagtacccacactgtgttgcatttagcaagttacaaaacaacaatcaattttgcaaagacatgattaccggttcttcaactgcagATGGACACAACGAGGCAGAGTTTGGGATGTCCTGGTGTGCTGGATTTGGTGGGGACTTCTACAACGCCTATTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG