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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAACAACGGAAAATGTTGGTGAAGCGACATTTAGCTATGACCGCTTGATATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcctgcacccgtccccccagcatccttgaagtggtgaattttctctagtgagtagttatggagttttttttcttggttccttgtaccagtaagt...

Basic information

species Zea mays
transcript GRMZM2G047310_T02
intron # 23
splice site 5'
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|6994020|gb|AW453234.1|AW453234
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|44901315|gb|CK827860.1|CK827860
EST:     TATCCAAATCCACCGATCCAGTTCGTGTGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|37392247|gb|CF633372.1|CF633372
EST:     CAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTG-TTTTGGCATNGACCAAGGA
genomic: CAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCAT-GACCAAGGA
EST: gi|89252837|gb|DY624623.1|DY624623
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|211011730|gb|FL062983.1|FL062983
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTTGCATGACCCAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|211541508|gb|FL473164.1|FL473164
EST:     TATCCAAATCCMCCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|14243479|gb|BG841162.2|BG841162
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|211156686|gb|FL406072.1|FL406072
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|211478872|gb|FL381839.1|FL381839
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|76914074|gb|DV165401.1|DV165401
EST:     CAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: CAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|60348915|gb|DN215888.1|DN215888
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|74240489|gb|DT648403.1|DT648403
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|67017477|gb|CO446226.1|CO446226
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|60346198|gb|DN213171.1|DN213171
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|60393923|gb|DN226793.1|DN226793
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|74240490|gb|DT648404.1|DT648404
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|5928766|gb|AW055983.1|AW055983
EST:     TATCCAAATCCCCCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|211246679|gb|FL466714.1|FL466714
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|67014678|gb|CO443427.1|CO443427
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|60350996|gb|DN217969.1|DN217969
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|93281334|gb|EB673598.1|EB673598
EST:     TATCCAAATCCCCCGATCCAGTTCGTGGGATGGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|6851640|gb|AW352650.1|AW352650
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTCCAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|6465597|gb|AW191192.1|AW191192
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|60394045|gb|DN226915.1|DN226915
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|6012269|gb|AW061811.1|AW061811
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|71760290|gb|DR958227.1|DR958227
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
EST: gi|149103859|gb|EE289270.2|EE289270
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGA
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGA
EST: gi|14243713|gb|BG841420.2|BG841420
EST:     TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAG                         GCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT
genomic: TATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

AGAAACAACGGAAAATGTTGGTGAAGCGACATTTAGCTATGACCGCTTGATATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGATGCATTCTACCGACAGCCAAATTGGAAGCAAGAACTACAGAAGCGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

AGAAACAACGGAAAATGTTGGTGAAGCGACATTTAGCTATGACCGCTTGATATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGATGCATTCTACCGACAGCCAAATTGGAAGCAAGAACTACAGAAGCGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

AGAAACAACGGAAAATGTTGGTGAAGCGACATTTAGCTATGACCGCTTGATATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGATGCATTCTACCGACAGCCAAATTGGAAGCAAGAACTACAGAAGCGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

AGAAACAACGGAAAATGTTGGTGAAGCGACATTTAGCTATGACCGCTTGATATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcct ... gattctgcagGCATACTTATCAGATAGTGAATTCCAAACTGTTTTTGGCATGACCAAGGATGCATTCTACCGACAGCCAAATTGGAAGCAAGAACTACAGAAGCGAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAACAACGGAAAATGTTGGTGAAGCGACATTTAGCTATGACCGCTTGATATCCAAATCCACCGATCCAGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgtgcctgcacccgtccccccagcatccttgaagtggtgaattttctctagtgagtagttatggagttttttttcttggttccttgtaccagtaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccccc