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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaaatagctgtcaattttttttgcagtgttgtggtttcaggtttcacctgactgagctattttttttgggcaatccttcatcaaatgcctgtgacaaactttataactgaactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCA

Basic information

species Zea mays
transcript GRMZM2G033828_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033828_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 16
----------gtaagtaaaatagctgtcaattttttttgcagtgttgtggtttcaggtttcacctgactgagctattttttttgggcaatccttcatcaaatgcctgtgacaaactttataactgaactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCA
            || |||| |      |  | |    |  | |||||   ||  |     ||||||| |    ||  | |  |||  | ||||| ||||| ||  |||||||      |||||||||   | |||||||| ||| | || ||||| |||||||||||||| ||||| || || || ||||| ||  | || || |||||||||||||||||||| |||| ||| |
gtacgcctcaagaaataaactgatctcccttgtgaagtttaatgttgcatttataatgaccacctgaatt--ttaactataatgg-tagtccttgatcaa-tgt-tgtgacat-tgcaataactgaatgtttcagATGGATACTTTGCTTTCCCCAAGCTCCAAGAGCTATTACGCCTGTGTAGGGGAGAGTACTCATGCATTTCAGAGCCCCTCCAAGGACCTTAAGGTTATAA
















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|30086964|gb|CB885172.1|CB885172
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|76933781|gb|DV173583.1|DV173583
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|30031712|gb|CB833563.1|CB833563
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|30087032|gb|CB885240.1|CB885240
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|30032038|gb|CB833889.1|CB833889
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|30088299|gb|CB886504.1|CB886504
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|29544714|gb|CB605094.1|CB605094
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|76933783|gb|DV173584.1|DV173584
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGG
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGG
EST: gi|27575967|gb|CA998661.1|CA998661
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|30088298|gb|CB886503.1|CB886503
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
EST: gi|30031776|gb|CB833627.1|CB833627
EST:     AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAG                         ATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC
genomic: AGGTTTCTGCTACCCATAACGTGTACGTCTCACCGCTACGGTCATCGAAGgtaagtaaaa ... aactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgggcaatccttcatcaaatgcctgtgacaaactttataactgaactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCA
                                    ttataac  putative branch site (score: 2)
                                               ctctcc  putative PPT
                               aaactttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaaatagctgtcaattttttttgcagtgttgtggtttcaggtttcacctgactgagctattttttttgggcaatccttcatcaaatgcctgtgacaaactttataactgaactctccagATGGACACTCTTCTGTCCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG