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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctaattttggaaaacttccataaactccaactatttttgtttcttgctgaagctgaactaaggttttgtgattacaaatttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTTCTTACTGTGCTTACTGGTACTGTTGTACTGCATTCTACAAGAGAACATG

Basic information

species Zea mays
transcript GRMZM2G097421_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097421_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g35570.1 (Oryza sativa), 3'ss of exon 7
gtattctaattttggaaaacttccataaactccaactatttttgtttc--ttgctgaagctgaactaaggttttgtgattacaaatttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTTCTTACTGTGCTTACTGGTACTGTTGTACTGCATTCTACAAGAGAACATG
|||| |   |||| | ||  ||||| |||  |||  || |||   | |  || ||  | |  || |  |    | || ||     |||    | |||| |||||||| |||||||||||||||||||| |||||||| ||||| ||||||||||||||| ||||||| |||||| ||||||||||||||||| |||
gtatgcaggttttagtaag-ttccacaaatgccagttagtttaagtccatttactagaacaaaaatttgagaatatgttttatggttt----ccagGATTGGTCTGGACAGAGTATAAGCAGTATTGCTTCTGAGATCTGTGGATTTCTTACTGTGCTTTCTGGTACCGTTGTATTGCATTCTACAAGAGAATATG
















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|149013792|gb|EE043259.2|EE043259
EST:     ACATCCCTCACAATTTTGGCAAGGGCCATAATGTTCAAGG                         GACGGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGGGGGGT
genomic: ACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAA-Ggtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTT-GTGGGT
EST: gi|149005297|gb|EE039846.2|EE039846
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|78118378|gb|DV536764.1|DV536764
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|149012853|gb|EE042695.2|EE042695
EST:     TGCGATGTTTACATCCCTCACAAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: TGCGATGTTTACATCCCTCAC-AATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|148947644|gb|EC893124.2|EC893124
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|86468982|gb|DY235352.1|DY235352
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|149101363|gb|EE187480.2|EE187480
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|94477225|gb|EB706183.1|EB706183
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|149070088|gb|EE158488.2|EE158488
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|44901394|gb|CK827939.1|CK827939
EST:     GGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: GGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|86471099|gb|DY237469.1|DY237469
EST:     TTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: TTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|148948890|gb|EC894304.2|EC894304
EST:     ATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|211094620|gb|FL143748.1|FL143748
EST:     TGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: TGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|94478877|gb|EB707835.1|EB707835
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|78123628|gb|DV542012.1|DV542012
EST:     ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: ATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
EST: gi|148951156|gb|EC896835.2|EC896835
EST:     TTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG                         GACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT
genomic: TTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAGgtattctaat ... ttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtttcttgctgaagctgaactaaggttttgtgattacaaatttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTTCTTACTGTGCTTACTGGTACTGTTGTACTGCATTCTACAAGAGAACATG
                                    attacaaatttacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctaattttggaaaacttccataaactccaactatttttgtttcttgctgaagctgaactaaggttttgtgattacaaatttacaactagGACTGGTCTGGGCAGAGTATAAGCAGTATTGCCTCTGAGATTTGTGGGTTTCTTACTGTGCTTACTGGTACTGTTGTACTGCATTCTACAAGAGAACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA