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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaatatagctctctttagatgcacaatttatttttttatgtgctcaatttattttgcttatctgagaacttctggcccttgttctcatttttatatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCACCACCCCATCAGTCGTTTTGCCCCGCATTCCAAAGAAAACGGGGATCCTC

Basic information

species Zea mays
transcript GRMZM2G039889_T02
intron # 9
splice site 3'
intron type U2

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|78107919|gb|DV526337.1|DV526337
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|67022594|gb|CO451343.1|CO451343
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|76910226|gb|DV163762.1|DV163762
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|78107918|gb|DV526336.1|DV526336
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|76284975|gb|DV024543.1|DV024543
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|211026941|gb|FL261358.1|FL261358
EST:     AACCTTTTTCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|50336508|gb|CO531634.1|CO531634
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAN
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|30032149|gb|CB834000.1|CB834000
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|78123847|gb|DV542231.1|DV542231
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTTTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|31353590|gb|CD437947.1|CD437947
EST:     GAAACTGTTTGTGAT                         TTTTACATGAAGACACCTTCTAAGC-AGTATTCTCAGAAATGCAAGTTTCA
genomic: GAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCT-TGCAAGTATTCTCAGAAATGCAAGTTTCA
EST: gi|116824796|gb|EC868448.1|EC868448
EST:     AGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGC-AGTTTCAC
genomic: AGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|88758185|gb|DY542326.1|DY542326
EST:     CAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATT                         TTTTACATGAAGACAGGATCTGGCAAGTATTTTCAGAAATGCAAGTTTCA
genomic: CAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGA-Tgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCA
EST: gi|78115266|gb|DV533654.1|DV533654
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|31612380|gb|CD569002.1|CD569002
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|76016911|gb|DT944081.1|DT944081
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|71299499|gb|DR785760.1|DR785760
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|31910879|gb|CD651644.1|CD651644
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|71326312|gb|DR799844.1|DR799844
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|60400549|gb|DN233356.1|DN233356
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|211213178|gb|FL436853.1|FL436853
EST:     AACCTTTTTCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
EST: gi|71762950|gb|DR960887.1|DR960887
EST:     AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT                         TTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC
genomic: AACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGATgtatgtaata ... tatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttgcttatctgagaacttctggcccttgttctcatttttatatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCACCACCCCATCAGTCGTTTTGCCCCGCATTCCAAAGAAAACGGGGATCCTC
                                       tttttat  CT-rich tract
                                 ttctcatttttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaatatagctctctttagatgcacaatttatttttttatgtgctcaatttattttgcttatctgagaacttctggcccttgttctcatttttatatactgcagTTTTACATGAAGACAGGATCTTGCAAGTATTCTCAGAAATGCAAGTTTCACCACCCCATCAGTCGTTTTGCCCCGCATTCCAAAGAAAACGGGGATCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA