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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACGTAGTCTGCCCCAACTGCGGCCACGCCGCCGTCCTCGGCGAGATGTCGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccgcctcggccgctccctccctagtccctacctacttagctcgctgcttaaaccctaagcgccacactgcactgcatgaaagaatcctgggctaacactcttcatccatccag

Basic information

species Zea mays
transcript GRMZM2G123140_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123140_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 5'ss of exon 5
CAACGTAGTCTGCCCCAACTGCGGCCACGCCGCCGTCCTCGGCGAGATGTCGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccgcctcggccgctccctccctagtccctacctacttagctcgctgcttaaaccctaagcgccacactgcactgcatgaaagaatcctgggctaacactcttcatccatccag
|||||| |||||||||||||||||||||||||||||||||| ||| ||||| |||||||||||||||||||||||||| ||||| |||||||| |||||||| | |            |||||||    |  ||||||||||     ||  | |  |  ||| |  |   | ||| | |   ||  | |  ||||||    |                  
CAACGTCGTCTGCCCCAACTGCGGCCACGCCGCCGTCCTCGCCGACATGTCCTACGAGGAGCAGCAGCTCCGCATCGAGAACGCCAGGCTCAAAGACGAGgtcgcta-----------gctcccta---aaaccctacctacc--attcattcccaattcccaacacataatactcctcc-tatatatgcttcctggctgcag-----------------
















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|78084627|gb|DV513020.1|DV513020
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|50324011|gb|CO519137.1|CO519137
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|71764164|gb|DR962101.1|DR962101
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|93281069|gb|EB673333.1|EB673333
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|78074346|gb|DV502780.1|DV502780
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|148938577|gb|EC882901.2|EC882901
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|50330271|gb|CO525397.1|CO525397
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|86472399|gb|DY238769.1|DY238769
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|89250163|gb|DY621949.1|DY621949
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|78083048|gb|DV511441.1|DV511441
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|50322570|gb|CO517696.1|CO517696
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|50323712|gb|CO518838.1|CO518838
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|93013152|gb|EB638672.1|EB638672
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|76294065|gb|DV033633.1|DV033633
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|76291558|gb|DV031126.1|DV031126
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|93013982|gb|EB639502.1|EB639502
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGGTACGGCGGCGGCCGACAGCC
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCC-GGTACGGCGGCGGCCGACAGCC
EST: gi|88754724|gb|DY538865.1|DY538865
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|88756590|gb|DY540731.1|DY540731
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|50335383|gb|CO530509.1|CO530509
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|76922345|gb|DV168961.1|DV168961
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|149087104|gb|EE176643.2|EE176643
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|148953385|gb|EE152879.2|EE152879
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|148954731|gb|EC900184.2|EC900184
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|33467199|gb|CF244248.1|CF244248
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|71426041|gb|DR807091.1|DR807091
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|50333731|gb|CO528857.1|CO528857
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|71758544|gb|DR956481.1|DR956481
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|38687296|gb|CK144327.1|CK144327
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
EST: gi|71317347|gb|DR795368.1|DR795368
EST:     CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAG                         CTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG
genomic: CGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccg ... atccatccagCTCGACCGCTTGGCGTGCATCGCGACCCGGTACGGCGGCGGCCGACAGCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACGTAGTCTGCCCCAACTGCGGCCACGCCGCCGTCCTCGGCGAGATGTCGTACGAGGAGCAGCAGCTCCGCATCGAAAACGCTAGGCTCAAGGACGAGgttggtgccgcctcggccgctccctccctagtccctacctacttagctcgctgcttaaaccctaagcgccacactgcactgcatgaaagaatcctgggctaacactcttcatccatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC