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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctttttttacccttttttactagtcagtctgggtttgggtagtccttaaaccagtgaaatgccttgcaaacatcaacataaatttcttgtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA

Basic information

species Zea mays
transcript GRMZM2G139894_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 16
atctttttttacccttttttactagtcagtctgggtttgggtagtccttaaaccagtgaaatgccttgcaaacatcaacataaatttcttgtg--tccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA
         ||  |   ||   |  |  || |        |||  |  ||   |      ||  || |||||  | ||  ||  |||||| ||  || |||||||||| |||| |||||||| |  |||||||| ||||| ||||||||| |||| || |||||||| ||||||||||| |   ||||||||||||||||| 
gctcaaacctatgccccttcctttctttgttttcaccaatgtaa-ctgtagttcctcaccatttct-gcaaattttaaagtatgtttcttctgcctctacagAATTTCAGGAAATACATGACCTATAAGAAGGATTACAATGAGCTGCTCTTGCTTCTTCTGCGCACCCTGGTCAAGGATGTGCTGCACTTCGAAGAAATCG

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 15
atctttttttacccttttttactagtcagtct-----gggtttgggtagtccttaaaccagtgaaatgccttgcaaacatcaacataaattt--cttgtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA
         |||| |||| |  | || | ||       | || | | | |   ||    |   | ||||  |  |  | |   | |||| |   ||||      ||||  ||  | ||||| ||||| ||||||||||||||||| || ||||||||     | || |||   || || ||| | ||  |||| || ||||||||  
-------actaccattttgtgattgtgattccctttaagattagtggaattggtactggaaaaatatgctcttgagtccttcccctaaactgtgcttgctgttgcagAGCTTTAGAAAGTATATGACTTTCAAGAAGGACTACAATGAACTGCTCCTTTATATTCTTCGCGAGCTTGTAAAGAATGCTTTGCATTTTGAAGAAATTG
















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|33093214|gb|CF053208.1|CF053208
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|74242322|gb|DT650236.1|DT650236
EST:     ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|74242323|gb|DT650237.1|DT650237
EST:     ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|32931979|gb|CF036791.1|CF036791
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|32934497|gb|CF039309.1|CF039309
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|18450515|gb|BM428793.1|BM428793
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
EST: gi|32932452|gb|CF037264.1|CF037264
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|32932490|gb|CF037302.1|CF037302
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGT
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGT
EST: gi|32911609|gb|CF016421.1|CF016421
EST:     ACTCTTTTATTTCGACTCAGAAATTCGGTGTGCAGAAAGCACTCCAAAAG                         AATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG
genomic: ACTCTTTTATTTCGACTCAGAAGTTCGGTGTGCAGAAAGCACTTCAAAAGgtaagttttg ... gtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttaaaccagtgaaatgccttgcaaacatcaacataaatttcttgtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA
                                       tttcttgt  CT-rich tract
                            atcaacataaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctttttttacccttttttactagtcagtctgggtttgggtagtccttaaaccagtgaaatgccttgcaaacatcaacataaatttcttgtgtccacagAATTTCCGGAAGTACATGACATTCAAGAAGGACTACAACGAGCTGCTCCTGCTGCTCCTGCGCACACTGGTCAAGGACGCCGTGCACTTCGAAGAAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA