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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacaatgacaaccgtgaaatttaaaaacatatactcaaagtaccacttttagattatttctgcatttgaccactaatattaaaggttttgattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG

Basic information

species Zea mays
transcript GRMZM2G036861_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------ccacaatgacaaccgtgaaatttaaaaacatatactcaaagtaccacttttagattatttctgcatttgaccactaat--attaaaggttttgatta-catagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG
                                                        ||  || |      || |||      |        || | ||  | | |||  |||  | | ||    |    |||   |   ||  ||||||||| || |||||||| || ||||||||||||||| || |||| ||||||||||| || ||||||||||| ||||||||||||||||
gtttgtctcttgaaaaatccattatttctgtgctgacagctggcttctgtcaaaaacaggattatgcaaatgcaatcctgctaacctcttgcagaatatgattgttatgttacat-tacaccataatgttaactgacataaaattttgattatcacagACGGCCAGGCCAGAGCAGAATAACCACCCCAAGAAAGGAGACTGACACTTGCAAAATTCTTTCAGGGACACATGAAG
















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|211106359|gb|FL258168.1|FL258168
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|148952455|gb|EC898280.2|EC898280
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|211106356|gb|FL258165.1|FL258165
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGTCAGAGCAGAATAAC
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAAC
EST: gi|148950436|gb|EC896004.2|EC896004
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|71442819|gb|DR823869.1|DR823869
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATACCCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149088416|gb|EE177517.2|EE177517
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149096924|gb|EE182722.2|EE182722
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|211106357|gb|FL258166.1|FL258166
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149088025|gb|EE177228.2|EE177228
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149089246|gb|EE178450.2|EE178450
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149106625|gb|EE188518.2|EE188518
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|148950790|gb|EC896395.2|EC896395
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|148951094|gb|EC896759.2|EC896759
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149111173|gb|EE294669.2|EE294669
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|211106358|gb|FL258167.1|FL258167
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149084565|gb|EE174034.2|EE174034
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|76281790|gb|DV021358.1|DV021358
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149067437|gb|EE287007.2|EE287007
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|148936477|gb|EC880584.2|EC880584
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149098825|gb|EE184838.2|EE184838
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|211106354|gb|FL258163.1|FL258163
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|76934911|gb|DV174083.1|DV174083
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|211106355|gb|FL258164.1|FL258164
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGTCAGAGCAGAATAACCTCCACAAGAAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|211106349|gb|FL258158.1|FL258158
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|148957149|gb|EC903140.2|EC903140
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|211106350|gb|FL258159.1|FL258159
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149071022|gb|EE159425.2|EE159425
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|211106353|gb|FL258162.1|FL258162
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
EST: gi|149036977|gb|EE155215.2|EE155215
EST:     CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAG                         ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG
genomic: CCTAGAATTCCACTCACTGAGGCAGACCTACAAGTTGAACTCGATCGAAGgtgcacttat ... gattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttagattatttctgcatttgaccactaatattaaaggttttgattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG
                             taatattaaaggtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacaatgacaaccgtgaaatttaaaaacatatactcaaagtaccacttttagattatttctgcatttgaccactaatattaaaggttttgattacatagACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA