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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctaacacactcccaaccacttctactgtatctttcagcagtaactgtgtttttcctttatataaatatacatgatgttaattgacatgacttttgatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCGAGCCTGTTCCATGCACCTGCGATCTCAATGCACGAAGATGCAGTTGAAT

Basic information

species Zea mays
transcript GRMZM2G415846_T01
intron # 13
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|211144259|gb|FL374578.1|FL374578
EST:     TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAG                         GTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
genomic: TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
EST: gi|101383979|gb|EB814044.1|EB814044
EST:     TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAG                         GTGTGCTTGCCCTTCA-TAGTGAATGAGTTCCTGAGACAGGCTACAGCTGC
genomic: TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCC-TTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGC
EST: gi|93283859|gb|EB676123.1|EB676123
EST:     TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAG                         GTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
genomic: TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
EST: gi|211216852|gb|FL374182.1|FL374182
EST:     TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAG                         GTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
genomic: TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
EST: gi|6918320|gb|AW399850.1|AW399850
EST:     TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAG                         GTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
genomic: TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
EST: gi|26457293|gb|CA828876.1|CA828876
EST:     TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAG                         GTGTGCTTGCCTTCAATAGTGAATGAGT
genomic: TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGT
EST: gi|211405623|gb|FL391563.1|FL391563
EST:     TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAG                         GTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
genomic: TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
EST: gi|14245072|gb|BG873654.1|BG873654
EST:     TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAG                         GTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG
genomic: TTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCG

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: 407

CTTTCGGTTAAGATCTATTATGGACTACCCAAATCTTAAACAACAACTTTTTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCGAGCCTGTTCCATGCACCTGCGATCTCAATGCACGAAGATGCAGTTGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 310

CTTTCGGTTAAGATCTATTATGGACTACCCAAATCTTAAACAACAACTTTTTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCGAGCCTGTTCCATGCACCTGCGATCTCAATGCACGAAGATGCAGTTGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 176

CTTTCGGTTAAGATCTATTATGGACTACCCAAATCTTAAACAACAACTTTTTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCGAGCCTGTTCCATGCACCTGCGATCTCAATGCACGAAGATGCAGTTGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 425

CTTTCGGTTAAGATCTATTATGGACTACCCAAATCTTAAACAACAACTTTTTCGAATGCGAATCCGGGATATCTTGGTCCACCCATTGCAGCCATTAAAGgtctaacaca ... gatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCGAGCCTGTTCCATGCACCTGCGATCTCAATGCACGAAGATGCAGTTGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctttatataaatatacatgatgttaattgacatgacttttgatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCGAGCCTGTTCCATGCACCTGCGATCTCAATGCACGAAGATGCAGTTGAAT
      tttatataaatataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctaacacactcccaaccacttctactgtatctttcagcagtaactgtgtttttcctttatataaatatacatgatgttaattgacatgacttttgatgttatagGTGTGCTTGCCTTCAATAGTGAATGAGTTCCTGAGACAGGCTACAGCTGCGAGCCTGTTCCATGCACCTGCGATCTCAATGCACGAAGATGCAGTTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG