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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaggacaccatcactgccctaatgtttcaagtgtgtatagcactaacatgtttgctaactaaaaactgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGAACAAACTCAGACAGATGTTACAGGAGACCAGTCAAGGTTTTCACCGCCG

Basic information

species Zea mays
transcript GRMZM2G040720_T01
intron # 13
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|32931165|gb|CF035977.1|CF035977
EST:     CTTGAATGTCAAAACAAATGTCATCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCCTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|60338335|gb|DN205308.1|DN205308
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|37381459|gb|CF627617.1|CF627617
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|37390531|gb|CF632497.1|CF632497
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|211465177|gb|FL447936.1|FL447936
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|60341736|gb|DN208709.1|DN208709
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         ------CGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|71305468|gb|DR788864.1|DR788864
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|60344633|gb|DN211606.1|DN211606
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|211412948|gb|FL027548.1|FL027548
EST:     ATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGCGCCAAGCAGAAAGTCGTGA
genomic: ATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|40336243|gb|CK370313.1|CK370313
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
EST: gi|86474242|gb|DY240612.1|DY240612
EST:     CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTG                         AAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA
genomic: CTTGAATGTCAAAACAAATGTCAGCTATCTCCGTCTGAGAGTGATTATTGgtgagtaagg ... ctgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtttcaagtgtgtatagcactaacatgtttgctaactaaaaactgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGAACAAACTCAGACAGATGTTACAGGAGACCAGTCAAGGTTTTCACCGCCG
                                             ctgctctc  CT-rich tract
                                   taactaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaaggacaccatcactgccctaatgtttcaagtgtgtatagcactaacatgtttgctaactaaaaactgctctcagAAATAGCGGTATTATTAGCTAAAGCAAATGGTGCCAAGCAGAAAGTCGTGAACAAACTCAGACAGATGTTACAGGAGACCAGTCAAGGTTTTCACCGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA