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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatcagatagcatgctctagttgatgaatacggatgccattattaacctaatgcctaatattttttatgtctctttccctttttatacatgtatgtatgcattacattatttcaattcaattttgtagaagACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATTTGCCTCAGACAGCG

Basic information

species Zea mays
transcript GRMZM5G807639_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 3
gtaattatcagatagcatgctctagttgatgaatacggatgccattattaacctaatgcctaatattttttatgtctctttccctttttatacatgtatgtatgcattacattatttcaattcaattttgtagaagACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATTTGCCTCAGACAGCG
                             ||| ||        || |||||     |||   | |  |||   || ||  ||| |  | || |||| |   |   ||  | |    |  | ||  | || |||||||||||||||||| || ||| | |||| ||||||| | ||||||||||||||||| || ||||  |
----------------------------gtgagtattagatgtataattaattatgtgctgtaaacattt---gtttcagtcc-taatgattcatgcactaaatgatcgcctctggttgaatc--tcttatagAAGACGCTATTACTTGCCAAATGCCTCTCCGTACCAACTCTGGAGTAGGTCATTTGCATCTGACAATG
















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|32862756|gb|CF002438.1|CF002438
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211494399|gb|FL426463.1|FL426463
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211042919|gb|FL416910.1|FL416910
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211275057|gb|FL384329.1|FL384329
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211011070|gb|FL374939.1|FL374939
EST:     CTTTGATTCCAGTTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211518170|gb|FL380292.1|FL380292
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211126388|gb|FL388997.1|FL388997
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211418591|gb|FL407188.1|FL407188
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211235901|gb|FL373720.1|FL373720
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|67031724|gb|CO460473.1|CO460473
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211490936|gb|FL402016.1|FL402016
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211094733|gb|FL379398.1|FL379398
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211317708|gb|FL417584.1|FL417584
EST:     CTTTGATTCCAGCTACTTCTCAATGCYCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211437186|gb|FL418966.1|FL418966
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|30306817|gb|CD001490.1|CD001490
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|37420219|gb|CF647798.1|CF647798
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211479894|gb|FL423794.1|FL423794
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211137577|gb|FL389523.1|FL389523
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         ACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATT
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATT
EST: gi|211157939|gb|FL380349.1|FL380349
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|31349005|gb|CD433362.1|CD433362
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211288450|gb|FL410952.1|FL410952
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211142865|gb|FL377125.1|FL377125
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTNGTACCAAGTTTGGAGTAGGT
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCT-GTACCAAGTTTGGAGTAGGT
EST: gi|211530093|gb|FL390761.1|FL390761
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211305586|gb|FL419218.1|FL419218
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211150258|gb|FL395029.1|FL395029
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|67025111|gb|CO453860.1|CO453860
EST:     CAGCTACTTCTCAATGCTCAAATCTGACAAG                         ACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATT
genomic: CAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATT
EST: gi|211050734|gb|FL374465.1|FL374465
EST:     CTTTGATTCCAGCTACTTCTCANTGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTA
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTA
EST: gi|93017175|gb|EB642695.1|EB642695
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211347968|gb|FL368837.1|FL368837
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211431976|gb|FL418926.1|FL418926
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211539307|gb|FL400264.1|FL400264
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211002857|gb|FL384096.1|FL384096
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211511665|gb|FL408091.1|FL408091
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG                         AAGACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGgtaattatca ... tttgtagaagA---CGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTC
EST: gi|211441962|gb|FL416333.1|FL416333
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|28187901|gb|CB179511.1|CB179511
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga
EST: gi|211063833|gb|FL423073.1|FL423073
EST:     CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG                       
genomic: CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAGgtaattatca ... tttgtaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctttttatacatgtatgtatgcattacattatttcaattcaattttgtagaagACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATTTGCCTCAGACAGCG
                        attacattatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattatcagatagcatgctctagttgatgaatacggatgccattattaacctaatgcctaatattttttatgtctctttccctttttatacatgtatgtatgcattacattatttcaattcaattttgtagaagACGCTATTACTTACCTAATCCATCTCTGTACCAAGTTTGGAGTAGGTCATTTGCCTCAGACAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG