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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatatttcgagcggaacagcttcgtattatttgcgccggcgaaatttctggctcgtttgtccccgcggttctgctgaggccagatttcctcctgcggcgttgaattgcgcgctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGATGCTCATCGACGGGGAGGTGGCGGCCGTCGCGGATGGTGGGCACTATGAC

Basic information

species Zea mays
transcript GRMZM5G806449_T02
intron # 1
splice site 3'
intron type U2

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|211339792|gb|FK980808.1|FK980808
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|211339790|gb|FK980806.1|FK980806
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|211339794|gb|FK980810.1|FK980810
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|33942501|gb|CF349101.1|CF349101
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGA
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGG-TTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGA
EST: gi|211339793|gb|FK980809.1|FK980809
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|211337407|gb|FK980805.1|FK980805
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|211339796|gb|FK980812.1|FK980812
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|211337405|gb|FK980803.1|FK980803
EST:     ACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGGCGAGAAAGA
genomic: ACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCAT-GGCGAGGAAGA
EST: gi|40485831|gb|CK394761.1|CK394761
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGA
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTT-GTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGA
EST: gi|33942302|gb|CF348902.1|CF348902
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGA
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGG-TTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGA
EST: gi|148945432|gb|EC890664.2|EC890664
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|211337397|gb|FK980795.1|FK980795
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|211337400|gb|FK980798.1|FK980798
EST:     ACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: ACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|148969995|gb|EE020910.2|EE020910
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|211337398|gb|FK980796.1|FK980796
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|148960879|gb|EE011558.2|EE011558
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|33101538|gb|CF061498.1|CF061498
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGAT
EST: gi|111991059|gb|EE331961.1|EE331961
EST:     GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAG                         GGTTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGA
genomic: GGAAGCACCGGTGACGAAGCCTTCCGTGTCATCACTCATCAGGATCTCAGgtgcatattt ... ctcgacctagGG-TTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttctgctgaggccagatttcctcctgcggcgttgaattgcgcgctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGATGCTCATCGACGGGGAGGTGGCGGCCGTCGCGGATGGTGGGCACTATGAC
                                 ttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatatttcgagcggaacagcttcgtattatttgcgccggcgaaatttctggctcgtttgtccccgcggttctgctgaggccagatttcctcctgcggcgttgaattgcgcgctcgacctagGGTTTTGTTTCGTTTCGCGGGCGTTGGGAATCCATCCATGGCGAGGAAGATGCTCATCGACGGGGAGGTGGCGGCCGTCGCGGATGGTGGGCACTATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG