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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttacatacgagctcctctcctgcctcctatctctaccacctcgctcttgccggcttgtatgtaacaacgtatctgactggtggccggccggctcgctctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGCAACCGGACGGGGCAGCCCTACATCCTGCAGACCAACGTGTTCACCGGCG

Basic information

species Zea mays
transcript GRMZM2G004699_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004699_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g33270.1 (Oryza sativa), 3'ss of exon 1
gtacgttacatacgagctcctctcctgcctcctatctctaccacctcgctcttgccggcttgtatgtaacaacgtatctgactggtggccggccggctcgctctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGCAACCGGACGGGGCAGCCCTACATCCTGCAGACCAACGTGTTCACCGGCG
          ||||  | || |   |||  |||    ||    ||   ||  | |  | | | |  |  | | | || ||  ||||        |  | |    || ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||| |||| |||||||||||||| ||||| ||| ||||||
---------gtacgc-cgccgccattgctccctgatcctcttccccttctgcttcttgatcggagat--cgatg-atgtg--tggttttt--ttgcattggggaatttgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGGAACAGGACGGGGGAGCCGTACATCCTGCAGACGAACGTCTTCTCCGGCG

upper sequence: GRMZM2G004699_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S309_38V6.2 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------gtacgttac-atacgagctcctctcctgcctcctatctctac----cacctcgctcttgccg-gcttgtatgtaacaacgtatc-tgactggtggccggccggctcgctctat--ctgcagCTGTCGTCGCAGA-ACTCGGA--GCACGACGAGATCGACTTCGAGTTCCTGGGCAACCGGACGGGGCAGCCCTACATCCTGCAGACCAACGTGTTCACCGGCG
                                                                       ||| |  | | |    || | |||  |   |     |     |   | | ||   |||  ||| ||   | |||  |      |||    |    |     |  ||| |   || || ||||||| |||| ||  |||   || |||||||| ||||| |||||||| || ||   | |||||||||||||||||||||| ||||| || |   |     
gtaaccccgataccactgacttgactattagtgttctatttcagagatgaagttacgtgcacagaagaattgttgctgttcaattgtctgttctgatttgcagtagcatgctgcgggtagatcacaccgcacttctagagagcaatattctgcaactttcagtttacaaataccttctgtgattgtagATGTCGTCACAGACACCAGGATTACATGACGAGATGGACTTTGAGTTCCTTGGAAATGTGTCGGGGCAGCCCTACATCCTGCAAACCAATGTCTATGCGA---
















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|20301243|gb|BQ164186.1|BQ164186
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|33467747|gb|CF244796.1|CF244796
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|9255437|gb|BE345905.1|BE345905
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|71439011|gb|DR820061.1|DR820061
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|22546122|gb|BU098443.1|BU098443
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|22819448|gb|BU499538.1|BU499538
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211298985|gb|FL169197.1|FL169197
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|89761345|gb|DY689393.1|DY689393
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|29130857|gb|CB381561.1|CB381561
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211298983|gb|FL169195.1|FL169195
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|23357642|gb|BU645291.1|BU645291
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211298979|gb|FL169191.1|FL169191
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|50326237|gb|CO521363.1|CO521363
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211296845|gb|FL169184.1|FL169184
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|37421332|gb|CF648364.1|CF648364
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTAC-AGTTCCTGGG
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTT-CGAGTTCCTGGG
EST: gi|211296849|gb|FL169188.1|FL169188
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211298984|gb|FL169196.1|FL169196
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|26456139|gb|CA827722.1|CA827722
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|60343742|gb|DN210715.1|DN210715
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|22133536|gb|BQ833767.1|BQ833767
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211298980|gb|FL169192.1|FL169192
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|22546396|gb|BU098707.1|BU098707
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|37423229|gb|CF649341.1|CF649341
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211298986|gb|FL169198.1|FL169198
EST:     ACATGAAGCTCKTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGGAGCACGACGAGATCGAC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGG-AGCACGACGAGATCGAC
EST: gi|148936701|gb|EC880831.2|EC880831
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|76018116|gb|DT945286.1|DT945286
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|50329318|gb|CO524444.1|CO524444
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211296847|gb|FL169186.1|FL169186
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|29130239|gb|CB380943.1|CB380943
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|148960072|gb|EE153316.2|EE153316
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
EST: gi|211296846|gb|FL169185.1|FL169185
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGGAGCACGACGAGATCGACTTCGAGTTCCTGGG
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGG-AGCACGACGAGATCGACTTCGAGTTCCTGGG
EST: gi|211296836|gb|FL169175.1|FL169175
EST:     ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTAC                         CTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC
genomic: ACATGAAGCTCGTCGGCGGCGACTCCGCGGGCACCGTCACGGCCTTCTACgtacgttaca ... ctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgtatgtaacaacgtatctgactggtggccggccggctcgctctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGCAACCGGACGGGGCAGCCCTACATCCTGCAGACCAACGTGTTCACCGGCG
                  atctgac  putative branch site (score: 3)
                                       ctcgctct  putative PPT
     tatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttacatacgagctcctctcctgcctcctatctctaccacctcgctcttgccggcttgtatgtaacaacgtatctgactggtggccggccggctcgctctatctgcagCTGTCGTCGCAGAACTCGGAGCACGACGAGATCGACTTCGAGTTCCTGGGCAACCGGACGGGGCAGCCCTACATCCTGCAGACCAACGTGTTCACCGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG