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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatgtggacatatcaacttggcttcttcttttgcatttttctgaactttatcattttgggccattttgcattcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAATTGAACCAAGCTATGGCAATCTTGCCCATACCATCAAGTGGCCCAGCAAC

Basic information

species Zea mays
transcript GRMZM2G088140_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088140_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g13170.2 (Oryza sativa), 3'ss of exon 9
gtatgtatgtggacatatcaacttggcttcttcttttgcatttttct-gaactttatcattttgggccat-tttgcattcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAATTGAACCAAGCTATGGCAATCTTGCCCATACCATCAAGTGGCCCAGCAAC
|| ||  | || |||| || |  ||| | ||  | || | | || || | | |  | | | ||      | ||||||| |  | ||| ||||||||||||| |||||||||||||||||  | |||  ||| ||| ||||| ||| ||||||||||| |||| ||  |||||||||| |||| | |
gtgtgcctatgaacatctcta--tggttgctagtgttccttattgctcggattgaaacctcttaatttttctttgcatcctgtcagAGGTTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAGTTGAATCAAACTATGGCAATCATGCCAATGACATCAAGTGGTCCAGTACC
















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|71442579|gb|DR823629.1|DR823629
EST:     GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGG                         ATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCTATCTGAGGGAAAAT
genomic: GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGGgtatgtatgt ... attcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAAT
EST: gi|60355311|gb|DN222284.1|DN222284
EST:     GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGG                         ATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAAT
genomic: GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGGgtatgtatgt ... attcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAAT
EST: gi|166519935|gb|EG106067.1|EG106067
EST:     GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGG                         ATGTTCGAAGTTCCCGGAATGGTGTA
genomic: GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGGgtatgtatgt ... attcaattagATGTTCGAAGTTCCCGGAATGGTGTA
EST: gi|32847056|gb|CD986737.1|CD986737
EST:     GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGG                         ATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAAT
genomic: GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGGgtatgtatgt ... attcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAAT
EST: gi|71772545|gb|DR970476.1|DR970476
EST:     GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGG                         ATGTTCGAAGTCCCCGGAATGGTGTATCACGTTTGCAATCTGA
genomic: GATTCACATCACAAGGAAAGTGGACAGGAACACGATGGGGgtatgtatgt ... attcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttttgcatttttctgaactttatcattttgggccattttgcattcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAATTGAACCAAGCTATGGCAATCTTGCCCATACCATCAAGTGGCCCAGCAAC
                   aactttatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatgtggacatatcaacttggcttcttcttttgcatttttctgaactttatcattttgggccattttgcattcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAATTGAACCAAGCTATGGCAATCTTGCCCATACCATCAAGTGGCCCAGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT