Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcctgatggacgaagctagttcttaagttgcataacacaaattctgtttaccgcacgaagatttcatttctgtccatagaagacatgcaaact...

Basic information

species Zea mays
transcript GRMZM2G130230_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 3
GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcctgatggacgaagctagttcttaagttgcataacacaaattctgtttaccgcacgaagatttcatttctgtc---catagaagacatgcaaact-----
||||| |||||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||||||  | | || |      ||||| | | ||      | |  || |  | ||| |      | ||   ||  | |||| |    ||||     |     || |     
GGATTTATACAATCAGGTGAAGTGCATATATTTGGGTATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttctaa------aagctgggtttttgacatcttggcatat-tgctgctgtattta-gatatttctacttcttttaaacatatctagccactgaatttgaat
















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|211003557|gb|FK956136.1|FK956136
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|74237092|gb|DT645006.1|DT645006
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|71449499|gb|DR830549.1|DR830549
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211398371|gb|FK956119.1|FK956119
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|50339442|gb|CO534568.1|CO534568
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|71447340|gb|DR828390.1|DR828390
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|89759526|gb|DY688327.1|DY688327
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|78083439|gb|DV511832.1|DV511832
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211398372|gb|FK956120.1|FK956120
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211398375|gb|FK956123.1|FK956123
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211398373|gb|FK956121.1|FK956121
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211003558|gb|FK956137.1|FK956137
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGARCCCCAGAAGATCTTTCAGAAATTTTG
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTG
EST: gi|211003549|gb|FK956128.1|FK956128
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTAATAA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTAATAA
EST: gi|211398378|gb|FK956126.1|FK956126
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211003552|gb|FK956131.1|FK956131
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTG
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTG
EST: gi|211003559|gb|FK956138.1|FK956138
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|71436592|gb|DR817642.1|DR817642
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211003548|gb|FK956127.1|FK956127
EST:     TATGCTAGATCAAATCTTTCTGATGATRGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211003556|gb|FK956135.1|FK956135
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211398377|gb|FK956125.1|FK956125
EST:     ATGCTAGATCAAATCTTTCTGATGATCGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAG
genomic: ATGCTAGATCAAATCTTTCTGATGAT-GGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAG
EST: gi|211398376|gb|FK956124.1|FK956124
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211003553|gb|FK956132.1|FK956132
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         T
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacag-
EST: gi|211003553|gb|FK956132.1|FK956132
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         T
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacag-
EST: gi|93283386|gb|EB675650.1|EB675650
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|78109778|gb|DV528194.1|DV528194
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|71449885|gb|DR830935.1|DR830935
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211398374|gb|FK956122.1|FK956122
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
EST: gi|211003555|gb|FK956134.1|FK956134
EST:     TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG                         GTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA
genomic: TATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcc ... ttttatacagGTATCTCAAAGGAGCCCCAGAAGATCTTTCAGAATTTTTGCAACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGGgtaatgatcctgatggacgaagctagttcttaagttgcataacacaaattctgtttaccgcacgaagatttcatttctgtccatagaagacatgcaaact

- - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacaaa