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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcaccccgcccttcggtggcttgctttgttacaccgggacccattgccggactaggattagggtttcattatccgtttgttctcgcgtcgaataggtggtgtgctgctcgatctgacgcgtgtttgtttgtttgtttgtttgtttcccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCCTATGGCACCTTGAAGGACTATAAGA

Basic information

species Zea mays
transcript GRMZM2G085670_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085670_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 1
--gtacgcaccccgcccttcggtggcttgctttgttacaccgggacccattgccggactaggattagggtttcattatccgtttgttctcgcgtcgaataggtggtgtgctgctcgatctgacgcgtgtttgtttgtttgtttgtttgtttcccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCCTATGGCACCTTGAAGGACTATAAGA
   || |   ||| |||  |  | |||     ||   | |||   | |   ||  |  |||| |||||||||                            || ||||  |  |     ||  | | | |   || | |    |||  |||    |   |||||| |||| || |||||  |||| || |||||| ||||||| |||||||||||||| || ||||||||||| ||||
gtataagggaccc-cccgcctctcgctccgcctgc-gccccgccgcgccgcgcgtgtttagggttagggtttt---------------------------gggggtggaccacctctcctcccccctctgatttcgatctaatgtcagttcgttgatgcagCTCACTGGAACGCAGTATGCGTCGTCTCTGGACGTGCTCCGCCTCTTCGCCTATGGGACATTGAAGGACTACAAGA
















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|101398140|gb|EB820944.1|EB820944
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|93013201|gb|EB638721.1|EB638721
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|50325881|gb|CO521007.1|CO521007
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|101390708|gb|EB817288.1|EB817288
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|32927905|gb|CF032717.1|CF032717
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|71330909|gb|DR802251.1|DR802251
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211281967|gb|FL132368.1|FL132368
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512613|gb|FL228206.1|FL228206
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|32927110|gb|CF031922.1|CF031922
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512616|gb|FL228209.1|FL228209
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512615|gb|FL228208.1|FL228208
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512618|gb|FL228211.1|FL228211
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|74236689|gb|DT644603.1|DT644603
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|32927326|gb|CF032138.1|CF032138
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|76936648|gb|DV174824.1|DV174824
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512612|gb|FL228205.1|FL228205
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512608|gb|FL228201.1|FL228201
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|76294401|gb|DV033969.1|DV033969
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512617|gb|FL228210.1|FL228210
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|89247571|gb|DY619357.1|DY619357
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|32928013|gb|CF032825.1|CF032825
EST:     CGGCCCTCTTCGGCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGGCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211281965|gb|FL132366.1|FL132366
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|71423346|gb|DR806010.1|DR806010
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|32927322|gb|CF032134.1|CF032134
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512610|gb|FL228203.1|FL228203
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211514961|gb|FL228214.1|FL228214
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|32927333|gb|CF032145.1|CF032145
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctgctcgatctgacgcgtgtttgtttgtttgtttgtttgtttcccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCCTATGGCACCTTGAAGGACTATAAGA
          atctgac  putative branch site (score: 3)
                                  tttgtttgtttccc  putative PPT
                      tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcaccccgcccttcggtggcttgctttgttacaccgggacccattgccggactaggattagggtttcattatccgtttgttctcgcgtcgaataggtggtgtgctgctcgatctgacgcgtgtttgtttgtttgtttgtttgtttcccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCCTATGGCACCTTGAAGGACTATAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG