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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACTTAAGCGCAGCCGGCCCCGGCCGGCATTCGCATCCGGTAGCTCGATCACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacactcgacgtcatgctccaattctgcttcgcggaacgtattcctgtcttcagttgccgattctttgtggagtttgggttggtggttggtgcggg...

Basic information

species Zea mays
transcript GRMZM2G006130_T01
intron # 1
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|148950545|gb|EC896122.2|EC896122
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|211169041|gb|FL129153.1|FL129153
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|148972033|gb|EE022867.2|EE022867
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|88755664|gb|DY539805.1|DY539805
EST:     GAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: GAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|211170726|gb|FL129169.1|FL129169
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|211170714|gb|FL129157.1|FL129157
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|148953656|gb|EC899016.2|EC899016
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|211170722|gb|FL129165.1|FL129165
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|149082080|gb|EE171257.2|EE171257
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|211169040|gb|FL129152.1|FL129152
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|148953586|gb|EC898940.2|EC898940
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|211170725|gb|FL129168.1|FL129168
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|148956552|gb|EC902392.2|EC902392
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|149079201|gb|EE168160.2|EE168160
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|211170720|gb|FL129163.1|FL129163
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|149100793|gb|EE186887.2|EE186887
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
EST: gi|211169043|gb|FL129155.1|FL129155
EST:     CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATG                         ACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA
genomic: CACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGA

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: 146

CTACTTAAGCGCAGCCGGCCCCGGCCGGCATTCGCATCCGGTAGCTCGATCACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGATCTCAAGCAAGCCTTCTCTGGTACAATCTTCTGCCTTCTGCTTCTATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 437

CTACTTAAGCGCAGCCGGCCCCGGCCGGCATTCGCATCCGGTAGCTCGATCACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGATCTCAAGCAAGCCTTCTCTGGTACAATCTTCTGCCTTCTGCTTCTATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 419

CTACTTAAGCGCAGCCGGCCCCGGCCGGCATTCGCATCCGGTAGCTCGATCACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGATCTCAAGCAAGCCTTCTCTGGTACAATCTTCTGCCTTCTGCTTCTATTC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 166

CTACTTAAGCGCAGCCGGCCCCGGCCGGCATTCGCATCCGGTAGCTCGATCACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacact ... tctccaacagACACACTCATTGCATTAGCGCCTACGCCTACCGCAAGTGGAAGCCTATGGATCTCAAGCAAGCCTTCTCTGGTACAATCTTCTGCCTTCTGCTTCTATTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACTTAAGCGCAGCCGGCCCCGGCCGGCATTCGCATCCGGTAGCTCGATCACTTCTTCCTCTGGATTTTGGGAAGGAGGCATCGGACGTCGGATGCATGgtgagacactcgacgtcatgctccaattctgcttcgcggaacgtattcctgtcttcagttgccgattctttgtggagtttgggttggtggttggtgcggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG