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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcgctctggctccgccgctaagttgtctcttgtcgcaccctacgtatctaagctgcatctgagtggatttcccattggtgggggacaataaacggtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCC

Basic information

species Zea mays
transcript GRMZM2G107106_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107106_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g41010.3 (Oryza sativa), 3'ss of exon 2
gtaggtcgctctggctccgccgctaagttgtctcttgtcgcaccctacgtatctaagctgcatctgagtggatttcccattggtgggggacaataaacggtg-ttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCC
||||||||||  | | | ||   |||  ||   |||  |      ||| | | ||||||||||||||| ||| || | |||  |||      ||  | |  |  || ||||  | ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| |||||||||||||  |||||||| ||||||||
gtaggtcgcttcgccgcggcgattaacctgcggctttcc----tttac-tgtttaagctgcatctgaggggaatttc-atttttggt-----atggatgacgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCC
















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|211112037|gb|FL390926.1|FL390926
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|87157624|gb|DY402413.1|DY402413
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|71765408|gb|DR963345.1|DR963345
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|26559761|gb|CA831996.1|CA831996
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|26559278|gb|CA831513.1|CA831513
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|71439462|gb|DR820512.1|DR820512
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|74243877|gb|DT651791.1|DT651791
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|74238077|gb|DT645991.1|DT645991
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|211157842|gb|FL370480.1|FL370480
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|148973713|gb|EE024841.2|EE024841
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|71439479|gb|DR820529.1|DR820529
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|31353283|gb|CD437640.1|CD437640
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|211431782|gb|FL408913.1|FL408913
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|37418046|gb|CF646683.1|CF646683
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|211019422|gb|FL374992.1|FL374992
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|37417359|gb|CF646332.1|CF646332
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|87157437|gb|DY402226.1|DY402226
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|211487436|gb|FL377864.1|FL377864
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|22542254|gb|BU092692.1|BU092692
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|22819789|gb|BU499879.1|BU499879
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCGCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|71313389|gb|DR793245.1|DR793245
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|71446967|gb|DR828017.1|DR828017
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|148947916|gb|EC893413.2|EC893413
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT
EST: gi|78115667|gb|DV534055.1|DV534055
EST:     GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACG                         GCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCGACT
genomic: GTCGACAGGCGCAGCCAGTCCGCCGGGAAGCGCGCCCGCACCGACGgtaggtcgct ... gtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctgcatctgagtggatttcccattggtgggggacaataaacggtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCC
                                              tgttctc  CT-rich tract
                                   acaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtcgctctggctccgccgctaagttgtctcttgtcgcaccctacgtatctaagctgcatctgagtggatttcccattggtgggggacaataaacggtgttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC