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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataacacttgtggtcatgtcccaatgtgttcaattttatgttctttgggtgggcttcgtgattatttggaaacattactggtggtacatggatatagctgtttagtgcaacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTTGCCTTGGTTCAATGGTGCTGCCTATGTTTACGACCATTTTGTGCGGCCA

Basic information

species Zea mays
transcript GRMZM2G047860_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 3
gtaaataacacttgtggtcatgtcccaatgtgttcaattttatgttctttgggtgggcttcgtgattatttggaaacattactggtggtacatggatatagctgt-ttagtgcaacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTTGCCTTGGTTCAATGGTGCTGCCTATGTTTACGACCATTTTGTGCGGCCA
                                                             |||||| |||       |||||  || | | |||| |||    | ||    || ||||  | | || | |  | || ||||||||||||  ||   ||| |||||||||||| |||||||| ||||||||| ||||||| ||||||||||||||||| ||||| ||| |||||||||| |||||||| || || ||||||||||||
------------------------------------------------------------tgtgatttttt-----ttttactattgatgc-tggagataaacatgttcacacatcaagaggat-aacaaaggattagatatgcttacttctgacggttgcttgcagGCTTCCTTTTTGGTCCTATGCAAAGTTGTTCTTCAACTGCTGGTTGGTCTTACCTTGCTTCCATGGTGCTGCTTATGTTTATGATCACTTTGTGCGGCCA
















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|33103480|gb|CF063440.1|CF063440
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|211371979|gb|FL186724.1|FL186724
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|32808662|gb|CD960896.1|CD960896
EST:     TGCTCATTTGTCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTA
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTA
EST: gi|33094100|gb|CF054094.1|CF054094
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|32917049|gb|CF021861.1|CF021861
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|33103180|gb|CF063140.1|CF063140
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|32933985|gb|CF038797.1|CF038797
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|33104168|gb|CF064128.1|CF064128
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCATATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|47961761|gb|CN844470.1|CN844470
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|32933645|gb|CF038457.1|CF038457
EST:     ACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: ACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|211371978|gb|FL186723.1|FL186723
EST:     TACTCATTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|94472096|gb|EB701054.1|EB701054
EST:     TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|76014693|gb|DT941863.1|DT941863
EST:     TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
EST: gi|86465815|gb|DY232188.1|DY232188
EST:     TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTG                         GCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT
genomic: TACTCGTTTATCACTTTGTTTGAGCTAACTTTTGCTCCAATTATCGAGTGgtaaataaca ... ttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTTGCCTTGGTTCAATGGTGCTGCCTATGTTTACGACCATTTTGTGCGGCCA
                             tgcttac  putative branch site (score: 2)
                                          tctttgttt  putative PPT
             aatagaaaactaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataacacttgtggtcatgtcccaatgtgttcaattttatgttctttgggtgggcttcgtgattatttggaaacattactggtggtacatggatatagctgtttagtgcaacaagttggtgaatagaaaactaaatatgcttactttagatctttgtttgcagGCTTCCATTTTGGTCGTATGCAAAGCTGTTCTTTAACTGCTGGTTGGTCTTGCCTTGGTTCAATGGTGCTGCCTATGTTTACGACCATTTTGTGCGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC