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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcagatccaaagcatccatgcagcagttgtgtccatttctccagagtccagtagatctgttgtcatcttcaactgattctatgtttctgaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCA

Basic information

species Zea mays
transcript GRMZM2G005036_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005036_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g44916.2 (Oryza sativa), 3'ss of exon 10
aatcagatccaaagcatccatgcagcagttgtgtccatttctccag--agtccagtagatctgttgtcatcttcaactgattcta---tgtttctgaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCA
       | | ||| |  |  |||   |    |   |||  |  ||  ||||   |  || ||              | ||  |    || ||       | |||||| || || ||||| ||||||||||| ||||||||||||||||| ||||||||||  ||||| |||||| |||| || ||| | || || ||| |||||
-----ttttctaagtaatccagcaattgcatagggtattaatttagatagtcacttccatttgccagagaaccttgtttatcttggagtgctttgtgttgtgcagGAAACCTATTGAGTACTTCCTGAAAACTGTTGAGGAGATCACTTTAAATGACATTTCTTCAACTGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCA
















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|40333865|gb|CK367935.1|CK367935
EST:     TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG                         GAAGCCCATTGATTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
genomic: TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAGgtacgagagt ... gaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
EST: gi|89758987|gb|DY687957.1|DY687957
EST:     TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG                         GAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
genomic: TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAGgtacgagagt ... gaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
EST: gi|30031571|gb|CB833422.1|CB833422
EST:     TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG                         GAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
genomic: TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAGgtacgagagt ... gaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
EST: gi|71438038|gb|DR819088.1|DR819088
EST:     TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG                         GAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
genomic: TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAGgtacgagagt ... gaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
EST: gi|32863948|gb|CF003630.1|CF003630
EST:     TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG                         GAAGCCCATTGATTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
genomic: TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAGgtacgagagt ... gaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
EST: gi|211146232|gb|FL303723.1|FL303723
EST:     TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG                         GAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
genomic: TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAGgtacgagagt ... gaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
EST: gi|40336960|gb|CK371030.1|CK371030
EST:     TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAG                         GAAGCCCATTGATTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA
genomic: TCTATAGCATCTGAAGATATTGGAAGACAGGTTCTTACTTATGGGGAAAGgtacgagagt ... gaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtccagtagatctgttgtcatcttcaactgattctatgtttctgaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCA
                           aactgat  putative branch site (score: 3)
                                            tgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcagatccaaagcatccatgcagcagttgtgtccatttctccagagtccagtagatctgttgtcatcttcaactgattctatgtttctgaaatttcagGAAGCCCATCGAGTATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG