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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAGCATTTGCATCCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattttttttaatccagaattgtcgcacctactgtccttttttattaaaatcttcagcaaatgtacaagctgttgttgatgcctcggatgcttgtcgaatatgaaaattttgttctctgatgcag

Basic information

species Zea mays
transcript GRMZM2G104166_T03
intron # 8
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|211163115|gb|FL067004.1|FL067004
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|67017186|gb|CO445935.1|CO445935
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|78543553|gb|DV621051.1|DV621051
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|6095746|gb|AW120413.1|AW120413
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|211163116|gb|FL067005.1|FL067005
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|211163114|gb|FL067003.1|FL067003
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|5895761|gb|AW037007.1|AW037007
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|91053809|gb|EB164227.1|EB164227
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|91056506|gb|EB166924.1|EB166924
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|5847057|gb|AW000136.1|AW000136
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|76283089|gb|DV022657.1|DV022657
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|148996412|gb|EE035707.2|EE035707
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
EST: gi|211188814|gb|FL462681.1|FL462681
EST:     CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAG                         GCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT
genomic: CCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 25

ACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAGCATTTGCATCCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCTGGTGACATTGTAATTGTCCGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

ACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAGCATTTGCATCCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCTGGTGACATTGTAATTGTCCGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

ACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAGCATTTGCATCCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCTGGTGACATTGTAATTGTCCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

ACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAGCATTTGCATCCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattt ... tctgatgcagGCCCTTGATTCATTTAATGCTGAAAGTGAGTTTGAGCTTACCTTGTCAGCTGGTGACATTGTAATTGTCCGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAGCATTTGCATCCACTTCTGTTAACGAGTCAGTCCAATCTGTCGATTTCTTCCTTGGAGAGgtatgaattttttttaatccagaattgtcgcacctactgtccttttttattaaaatcttcagcaaatgtacaagctgttgttgatgcctcggatgcttgtcgaatatgaaaattttgttctctgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA