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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagattaagctacaaatttaccctgttatattattggttgtgcatcaaccttcgatacattaagcctaaacttgcattctttgatctttgaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG

Basic information

species Zea mays
transcript GRMZM2G066496_T02
intron # 5
splice site 3'
intron type U2

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|32804124|gb|CD956360.1|CD956360
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|32859901|gb|CD999582.1|CD999582
EST:     GGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTT-TTTAAGACGACGGGCCAAAA
genomic: GGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|148954707|gb|EC900159.2|EC900159
EST:     AGAAGTTGGCAAGGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|32801615|gb|CD953851.1|CD953851
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCTTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|18164129|gb|BM333968.1|BM333968
EST:     GTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: GTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|118406764|gb|EH038212.1|EH038212
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|67022635|gb|CO451384.1|CO451384
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|89759755|gb|DY688471.1|DY688471
EST:     CTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: CTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|60359682|gb|DN226655.1|DN226655
EST:     TTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: TTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaccttcgatacattaagcctaaacttgcattctttgatctttgaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG
          atacattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagattaagctacaaatttaccctgttatattattggttgtgcatcaaccttcgatacattaagcctaaacttgcattctttgatctttgaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG