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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttaattcaacatcaaactagaacagacttgtagatattttgtatctcttgagtacactattccttcatctgaggcatgaagtttattttttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAATGGATTTACAAGGTACAGTCCTCTCCATCAGGCTAGCTTGTGTTTGGAC

Basic information

species Zea mays
transcript GRMZM2G101596_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101596_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 7
--------gcttaattcaacatcaaactagaacagacttgtagatattttgtatctcttgagtacactattccttcatctgaggcatgaagtttattttttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAATGGATTTACAAGGTACAGTCCTCTCCATCAGGCT-AGCTTGTGTTTGGAC
            | |   || | | ||    |    || |      |  || |||| ||| ||| || |||  |  | |||    ||||    | || ||| |||||||||||||| ||| |||||||||||||||| |||||  ||||  || || | |    || ||||  |   | |  |||| ||||||  | || ||||||   
gagttacaagccagtgacactttatacctttatttgctagctatattcctgcatct-ttgggtagacaattatt--aactgt--tatgag---tgttctttatgccagAATGATGATTTCATCGATTTAGTCTACCGGGAGATTGTGAAAGGATAGAATTAACATTTCAAGACAGCCTTCCTTCCAACAGGCTTGGTTTATGTTTGAC-
















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|6021492|gb|AW066420.1|AW066420
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|12968114|gb|BG265061.1|BG265061
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATAAACACACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|76909430|gb|DV163377.1|DV163377
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|16377525|gb|BI991975.1|BI991975
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAAACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|116817957|gb|EC860888.1|EC860888
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|89248633|gb|DY620419.1|DY620419
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGCCAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|149112670|gb|EE191400.2|EE191400
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|88754723|gb|DY538864.1|DY538864
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|211242534|gb|FL481658.1|FL481658
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
EST: gi|5922405|gb|AW055694.1|AW055694
EST:     CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAG                         AATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA
genomic: CAGCGCTGACTAGAGACAAAGTCAGAGATGCATTATTGAGACTTGTGGAGgtacactgtt ... tttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttgagtacactattccttcatctgaggcatgaagtttattttttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAATGGATTTACAAGGTACAGTCCTCTCCATCAGGCTAGCTTGTGTTTGGAC
                                      tttatttttt  CT-rich tract
                                atgaagtttatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttaattcaacatcaaactagaacagacttgtagatattttgtatctcttgagtacactattccttcatctgaggcatgaagtttattttttgtgccagAATGATGAATTCGTCGATTTAGTCTACCGCGAGATCATGAACAGACAGTAATGGATTTACAAGGTACAGTCCTCTCCATCAGGCTAGCTTGTGTTTGGAC

- - - - - -catcaaa
- - - - - - - - - - -gaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgaa