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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcacaatggttctaaatgacatttgctgaaaatgatactagtcagtttcgtgtgtcttctcttgaaaacttggtttgttttgtgttgttatgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCAATTTACAAGACTGATTATCCTCTGCCGACTCCTCAAAAACATTCGACGA

Basic information

species Zea mays
transcript GRMZM2G145376_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA19G32750.2 (Glycine max), 3'ss of exon 6
----ggcacaatggttctaaatgacatttgctgaaaatgatactagtcagtttcgtgtgtcttct--cttgaaaacttggtttgttttgtgttgttatgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTG--CAATTTACAAGACTGATTATCCTCTGCCGACTCCTCAAAAACATTCGACGA
      ||  | |   | | ||| | |||| || |  | ||  |  |     |   |   |  ||  ||   ||  ||  |||||||| ||||||        |||||||||| || || || ||||| ||||||||||||||||||| ||  |   ||    |    |  | | |     ||  |   |   ||  |  ||      
atgtttcattaagaaacaatatggcttttgatggatttaattttccttttcgtgaaggaacaccttgctacgaatgttaatttgttttctgttgtgg------cagCTTCGGGAAACATTCGTCAGCTTTACTGTCTACAAGGTGATTGATCTTTGTCAGGCAATGCAATGGCTCAGTGAATGATGGTACAGGAACGAGGTTTCTG--
















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|32803235|gb|CD955471.1|CD955471
EST:     AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACG                         CTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTA
genomic: AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACGgtaacgtact ... atgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTA
EST: gi|30307115|gb|CD001788.1|CD001788
EST:     AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACG                         CTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
genomic: AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACGgtaacgtact ... atgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
EST: gi|32788326|gb|CD940562.1|CD940562
EST:     AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACG                         CTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGGGATTA
genomic: AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACGgtaacgtact ... atgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTA
EST: gi|7136119|gb|AW498434.1|AW498434
EST:     AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACG                         CTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
genomic: AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACGgtaacgtact ... atgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
EST: gi|110538420|gb|EE042403.1|EE042403
EST:     AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACG                         CTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
genomic: AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACGgtaacgtact ... atgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
EST: gi|4776299|gb|AI665302.1|AI665302
EST:     AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACG                         CTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
genomic: AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACGgtaacgtact ... atgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
EST: gi|211453058|gb|FL439877.1|FL439877
EST:     AAGGGAATTGGCAGCTGCCYTTCATGCTCAGTTCAAGGATTGGTTATACG                         CTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
genomic: AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACGgtaacgtact ... atgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
EST: gi|78079826|gb|DV508238.1|DV508238
EST:     AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACG                         CTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA
genomic: AAGGGAATTGGCAGCTGCCCTTCATGCTCAGTTCAAGGATTGGTTATACGgtaacgtact ... atgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcgtgtgtcttctcttgaaaacttggtttgttttgtgttgttatgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCAATTTACAAGACTGATTATCCTCTGCCGACTCCTCAAAAACATTCGACGA
                                              tgtcctc  CT-rich tract
                             tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcacaatggttctaaatgacatttgctgaaaatgatactagtcagtttcgtgtgtcttctcttgaaaacttggtttgttttgtgttgttatgtcctcagCTTCGGGCAATATCCGCCAGCTCTACTGTCTACAAGGTGATTAATGGTGCAATTTACAAGACTGATTATCCTCTGCCGACTCCTCAAAAACATTCGACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC