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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgactgttcctgtttactatggaaatgtgaaagcagatgctgtttctcttgaggttgtcggtgtgctgactgaatctcaaattcgtttggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCTTATGATGGCCGCAAACTATCTGGACACTTGATGAGGAGCCTGAGGGGTA

Basic information

species Zea mays
transcript GRMZM2G059282_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059282_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 2
cttgactgttcctgtt-tactatggaaatgtgaaagcagatgctgtttctcttgaggttgtcggtgtgctgactgaatctcaaattcgtttggttgt---gtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCTTATGATGGCCGCAAACTATCTGGACACTTGATGAGGAGCCTGAGGGGTA
    | ||||  | |  || | |       | |||    | ||  |     || | ||   |  ||   |||||   |      || |||||||||     |||||||||||||||| | ||||||| ||| |||||||||||||| |||||||| |||||||| ||||||||||||||||| |||||||  |     |  || 
--caaatgttgttttaatattttacttcattcaaatttaaggcgctcatgtttaacgtcaac--tgaagtgactcggttgttgttttgtttggttggttgatagTGGGAAGGAGACATCTGAGTTTCAAATTGAACCGGAGATAACTCTGGAGCTGATGATGGCTGCAAACTATCTGGACACCTGATGAGATGAGGTGGAAGTG
















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|211141709|gb|FL287346.1|FL287346
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|13490768|gb|BG517532.1|BG517532
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|32937826|gb|CF042645.1|CF042645
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|32824382|gb|CD964104.1|CD964104
EST:     GATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: GATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|32938012|gb|CF042831.1|CF042831
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|211111068|gb|FL388616.1|FL388616
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|211214239|gb|FL370034.1|FL370034
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|211163296|gb|FL418729.1|FL418729
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGATAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGC
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGA-AGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGC
EST: gi|9461612|gb|BE453818.1|BE453818
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|211140277|gb|FL369583.1|FL369583
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|211491482|gb|FL425975.1|FL425975
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|7958448|gb|AW862750.1|AW862750
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|211431958|gb|FL418483.1|FL418483
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|211104586|gb|FL031932.1|FL031932
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|211468741|gb|FL385438.1|FL385438
EST:     TCCTCGAGAAGATCTGCCAGTATTTSSTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: TCCTCGAGAAGATCTGCCAGTATTTC-TATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
EST: gi|45846861|gb|CN070804.1|CN070804
EST:     ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAG                         TGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgc ... ggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcttgaggttgtcggtgtgctgactgaatctcaaattcgtttggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCTTATGATGGCCGCAAACTATCTGGACACTTGATGAGGAGCCTGAGGGGTA
                    tgctgac  putative branch site (score: 2)
                                 tcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgactgttcctgtttactatggaaatgtgaaagcagatgctgtttctcttgaggttgtcggtgtgctgactgaatctcaaattcgtttggttgtgtagTGGGAAGGAGACAGCGGAGTTTCCAATCGAACCGGAGATAACCCTGGAGCTTATGATGGCCGCAAACTATCTGGACACTTGATGAGGAGCCTGAGGGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - -gttcctg
- - - - - - - - - - - - - - - - - gcagatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgac