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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagcaaactattttgaaattaagtaaactatggggtattcattgaccctattcttaagattggctataactgatggttcccgttttctatgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGATCCTTCGAGTGCCCCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTT

Basic information

species Zea mays
transcript GRMZM5G862959_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862959_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g19350.1 (Oryza sativa), 3'ss of exon 6
aaagcaaactattttgaaat-taagtaaactatggggtattcattgaccctattcttaagattggctataactgatggttcccgttttctatgcttttc-----agGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGATCCTTCGAGTGCCCCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTT
      |  | |  |||||  |  | ||||| || |  ||| |||  | ||||  || |  || | |  |  ||     |   |||   |   | |||      |||||||||||||||||||||||  | |||||||||||||| |||| |||||||||||| |||||||| ||||||||||||||||||||||| |||||||||
-----gatgtttagtgaaacatttgcaaactctgag-cattaatttgcactataattgatgtttgttccacatgtaaaataatgttacttcccccttttgtaatagGAAGTACAAGTTGCCTATGTCAGATATTATTCCATTTCCAAAGAGAGGGGATCCTTCCAGTGCCCCAGATTTTGGGCAGGGTCGACAAGTCTTAGCTGTT
















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|78118927|gb|DV537311.1|DV537311
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|13126562|gb|BG317132.1|BG317132
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|67011782|gb|CO440531.1|CO440531
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|78084340|gb|DV512733.1|DV512733
EST:     TATGAAGTACTTGATGAAGAACCAGGTGAGGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|71332524|gb|DR803227.1|DR803227
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|13126563|gb|BG317133.1|BG317133
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|148974313|gb|EE025086.2|EE025086
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|67025991|gb|CO454740.1|CO454740
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|113703551|gb|EE681055.1|EE681055
EST:     TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: TATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
EST: gi|60345456|gb|DN212429.1|DN212429
EST:     GATGACGAAGAGAGCACTCAAAA                         GAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA
genomic: GATGACGAAGAGAGCACTCAAAAgtatgtgagg ... tgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accctattcttaagattggctataactgatggttcccgttttctatgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGATCCTTCGAGTGCCCCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTT
                       aactgat  putative branch site (score: 3)
                                ttcccgttttctatgc  putative PPT
     attcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagcaaactattttgaaattaagtaaactatggggtattcattgaccctattcttaagattggctataactgatggttcccgttttctatgcttttcagGAAGTACAAGTTGCCTATGTCTTACATTATTCCATTTCCGAAGAAAGGGGATCCTTCGAGTGCCCCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT