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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaagcttccgttacccctccagactcgctctcagtctcagctgctcgtaacacaccaccccggccctgaacctgtctcggttggtttgctttggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGGCCAGTCCTTCACAGGCAAAGAACGG

Basic information

species Zea mays
transcript GRMZM5G836250_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 8
gtaattaagcttccgttacccctccagactcgctctcagtctcagctgctcgtaacacaccaccccggccctgaacctgtctcggttggtttg-ctttggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGGCCAGTCCTTCACAGGCAAAGAACGG
     ||  | |        |   | |  || | ||  |  |  | | ||   ||     ||    |    | |||   |||   ||         ||||  ||  ||| | ||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||||||||||
----gtacacattaagcctactctcggcatctcacttcgcttatggtacttccaattt--catattga---taaacaattctgaattcaccaaatcttggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGGCCAGTCTTTCACAGGCAAAGAACGG

upper sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 11
gtaattaagcttccgttacccctccagactcgctctcagtctcagctgctcgtaacacaccaccccggccctgaacctg---tctcggttggtttgctttggttt-tgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGGCCAGTCCTTCACAGGCAAAGAACGG
     || | |   |||   ||||   | || || |  | || |   ||   |   | |    |    |  ||||  |    | | || ||  |||   || ||| |||||| ||||||| ||||| ||||| ||||| ||| | ||||| ||||||||||| ||||| ||||| ||||| ||||||
----gtatg-tcatgttcaacctctgcattcactttaggcctgaagagcatatccaagattgacaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG
















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|78105896|gb|DV524314.1|DV524314
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|76282214|gb|DV021782.1|DV021782
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|89759141|gb|DY688054.1|DY688054
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCTTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|93284534|gb|EB676798.1|EB676798
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|83279121|gb|DV943129.1|DV943129
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|50324976|gb|CO520102.1|CO520102
EST:     GGGGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|71768088|gb|DR966025.1|DR966025
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|86471231|gb|DY237601.1|DY237601
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|50331044|gb|CO526170.1|CO526170
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|149085229|gb|EE174736.2|EE174736
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCTTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|78113531|gb|DV531922.1|DV531922
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|148929799|gb|EE285436.2|EE285436
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|88752752|gb|DY536893.1|DY536893
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|71770842|gb|DR968779.1|DR968779
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|149088445|gb|EE177548.2|EE177548
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|86473014|gb|DY239384.1|DY239384
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|149064612|gb|EE286483.2|EE286483
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|71317307|gb|DR795338.1|DR795338
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|110201016|gb|EC882913.1|EC882913
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|94476278|gb|EB705236.1|EB705236
EST:     GGTGTGTCTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|50332538|gb|CO527664.1|CO527664
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|149099889|gb|EE185942.2|EE185942
EST:     GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
EST: gi|71314864|gb|DR794057.1|DR794057
EST:     GTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG                         TATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG
genomic: GTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCGgtaattaagc ... ggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacacaccaccccggccctgaacctgtctcggttggtttgctttggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGGCCAGTCCTTCACAGGCAAAGAACGG
 tcgtaac  putative branch site (score: 2)
                                               ttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaagcttccgttacccctccagactcgctctcagtctcagctgctcgtaacacaccaccccggccctgaacctgtctcggttggtttgctttggttttgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGGCCAGTCCTTCACAGGCAAAGAACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC