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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcgttcttctaggtggcttggttctcttcagatatactatgtcatgaccttgacatttgccgggaagttttacacagccactcttttgcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCAGACCCTTCTGTTTTCTTGATGGGAGAAGAG

Basic information

species Zea mays
transcript GRMZM2G043198_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g42410.1 (Oryza sativa), 3'ss of exon 2
tattcgttcttctaggtggcttggttct--cttcagatatactatgtcatgaccttgacatttgccgggaagttttacacagccactcttttgcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCAGACCCTTCTGTTTTCTTGATGGGAGAAGAG-------------------
||  |||  |||| |    | | |   |  | |    |  | ||     |  || |   |  | ||| ||  ||| ||        | | ||||| ||  |||| ||||| || |||||||||||| | ||  | ||||| || ||||| || ||||||||||||||||||||||||||||||                   
tacacgtgattcttgaatacatagacatgacgttctcttgagtacagt-tctccgttctacataccgtgagatttgacttgcaacttttcttgctcatc-agATGACTGTGCGTGAAGCATTGAATTCTGCCCTTGATGAGGAGATGTCTGCTGACCCTTCTGTTTTCTTGATGGGAGAAGAGGTTGGAGAATACCAAGGGG
















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|211444057|gb|FL415432.1|FL415432
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211273080|gb|FL371948.1|FL371948
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211491514|gb|FL426447.1|FL426447
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211003333|gb|FL404181.1|FL404181
EST:     TCCGCCCCGCCGCCGCTCCCGCCA-GACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|148930818|gb|EC873192.2|EC873192
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211084499|gb|FL378037.1|FL378037
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|32799489|gb|CD951725.1|CD951725
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|148953725|gb|EC899090.2|EC899090
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|32804720|gb|CD956956.1|CD956956
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|37426139|gb|CF650819.1|CF650819
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|38687965|gb|CK144996.1|CK144996
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|14997073|gb|BI319153.1|BI319153
EST:     TCCGCCCCGCCGCCGATCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|93281968|gb|EB674232.1|EB674232
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211431560|gb|FL401076.1|FL401076
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211311674|gb|FL419261.1|FL419261
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211503999|gb|FL380203.1|FL380203
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211056917|gb|FL385087.1|FL385087
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211395332|gb|FL395257.1|FL395257
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|8367328|gb|BE050273.1|BE050273
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGGATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211017664|gb|FL418154.1|FL418154
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGACAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211499368|gb|FL394923.1|FL394923
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211423792|gb|FL402788.1|FL402788
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211063939|gb|FL426137.1|FL426137
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211099620|gb|FL375433.1|FL375433
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211542664|gb|FL412592.1|FL412592
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211054277|gb|FL399886.1|FL399886
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211479962|gb|FL426376.1|FL426376
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|31357689|gb|CD442046.1|CD442046
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGGCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211530195|gb|FL395784.1|FL395784
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCAGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
EST: gi|211016844|gb|FL388973.1|FL388973
EST:     TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAG                         ATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA
genomic: TCCGCCCCGCCGCCGCTCCCGCCAGGACCTACTCCGCCGCGGCCAAGGAGgtgagcgcta ... gcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaccttgacatttgccgggaagttttacacagccactcttttgcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCAGACCCTTCTGTTTTCTTGATGGGAGAAGAG
     ccttgac  putative branch site (score: 4)
                                      ctcttttgcttattt  putative PPT
                                               ttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattcgttcttctaggtggcttggttctcttcagatatactatgtcatgaccttgacatttgccgggaagttttacacagccactcttttgcttatttagATAACTGTACGGGAAGCATTGAATACCGCATTAGATGAAGAAATGTCGGCAGACCCTTCTGTTTTCTTGATGGGAGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA