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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcctagattgctcagtattctcttggtgttcccgttgtatgtttaaaccaatagatctacttgttttatccgctaacaaactgttatacgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG

Basic information

species Zea mays
transcript GRMZM2G021742_T01
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|148969289|gb|EE020059.2|EE020059
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|91053554|gb|EB163972.1|EB163972
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|50326107|gb|CO521233.1|CO521233
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|60343545|gb|DN210518.1|DN210518
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACT
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACT
EST: gi|71446950|gb|DR828000.1|DR828000
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|60356065|gb|DN223038.1|DN223038
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|76918345|gb|DV167252.1|DV167252
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|4226387|gb|AI396494.1|AI396494
EST:     AAGGTCCTAAAGTAGATGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATG
EST: gi|113701906|gb|EE679410.1|EE679410
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|71761635|gb|DR959572.1|DR959572
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|211242314|gb|FL469535.1|FL469535
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|71317917|gb|DR795718.1|DR795718
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|211124519|gb|FL463077.1|FL463077
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|60356070|gb|DN223043.1|DN223043
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|4226377|gb|AI396484.1|AI396484
EST:     AAGGTCCTAAAGTAGATACTCCAACTCCTGAACAAATAAAAGCTATCAAG                         GCTGCTATTGCAAATG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATG
EST: gi|31364112|gb|CD448467.1|CD448467
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTTGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|71317919|gb|DR795719.1|DR795719
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|60397657|gb|DN230473.1|DN230473
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACT
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACT
EST: gi|5650116|gb|AI920476.1|AI920476
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTTGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|78117951|gb|DV536338.1|DV536338
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaccaatagatctacttgttttatccgctaacaaactgttatacgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
                            cgctaac  putative branch site (score: 2)
                  ttgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcctagattgctcagtattctcttggtgttcccgttgtatgtttaaaccaatagatctacttgttttatccgctaacaaactgttatacgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC