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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaactatacatgtgtacctctcgtcttatttgatcccattctttgcacttttgttcatctactagttgcactagtggagtaatctttttttcatcag

Basic information

species Zea mays
transcript GRMZM2G331032_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G331032_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 5'ss of exon 5
---------------------------------CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaactata---catgtgtacctctcgtct-tatttgatcccattctttgcacttttgttcatctactagttgcactagtggagtaatctttttttcatcag
                                 ||||| ||||| ||||||||||||||||||||||| ||| ||||||||||||| ||||||| |   | | |   ||  |  |  | || ||| ||||||  |  ||| |  ||| |  |    | |||  | ||  | || |     |        |  ||   
CCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAGgtgcctgttccaaatgccacctccaagtttcatctgtatttggacatattat--gcattgctagctagctagcatttctaataatcc--cagctcagcatagat---

upper sequence: GRMZM2G331032_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 5'ss of exon 5
---------------------------------CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaactatacatgtgtacctctcgtcttatttgatcccattctttg-cacttttgttcatctactagttgcactagtggagtaatctttttttcatcag
                                 ||||| || || ||||||||||||||||||||||| ||||  ||||| ||||||||||||  |      |   | | |   | |  | |   | |      || |  |  | |  || | || |   | |  | | |  | ||                  
CCAAAAGACAAACCTGTTCCAAATGCAACATTACAAGTTACAGGTGCTGTTGGTTGGAGAAGAGAGGGCCTTGCTTACAAAAAGAATGAGgtgagtgttgagtttctttctgtgtgt-atgtagatcggctaggttgtgcggtagtgatgat-attttgcattctctcaaacgcag------------------

upper sequence: GRMZM2G331032_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 5
---------------------------------CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaactatacatgtgt-----acctctcgtcttatttgatcccattctt-tgcacttttgttcatctactagttgcactagtggagtaatctttttttcatcag
                                 ||||| || || |||||||||||||| |||||||| ||||| || || |||||||||||| || | |  |   | | |     |  |  | |  |  ||     ||||||  || | |||||  |||||  |  || ||                           
CCTTCAGATAAACCAGTCCCCAATGCAACTTTACAAGTTACAGGTGCTGTTGGTTGGAGGAGAGAGGGCCTTGTTTATAAAAAGAATGAGgtgatttatccttttctttttctgcaattttccatggtgattttggtcattctgatggatttttga-catctgttcattacag--------------------------

upper sequence: GRMZM2G331032_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ22278 (Selaginella moellendorffii), 5'ss of exon 5
------------------------------------CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaactatacatgtgtacctctcgtcttatttgatcccattctttgcacttttgttcatctactagttgcactagtggagtaatctttttttcatcag
                                    |||||||| || || || || |||||||||||||| ||||| |||||||| ||||||||        | |  |  | |    || | || ||   | |  || ||||  |                                                  
CCCATAGATACAAGACCCCCAGCAAATGCTACTCTCCAAGTCACCGGTGCAGTGGGATGGAGAAGAGAGGGTCTTGTTTACAAGAAAAATGAGgtttgctgtttttcaaactttgatgctagactaat---accgtatgctttctag-------------------------------------------------

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|71445146|gb|DR826196.1|DR826196
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|149090427|gb|EE179737.2|EE179737
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|76937034|gb|DV175018.1|DV175018
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|71304030|gb|DR788136.1|DR788136
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|91054998|gb|EB165416.1|EB165416
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|149083894|gb|EE173269.2|EE173269
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|76282279|gb|DV021847.1|DV021847
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|32935086|gb|CF039898.1|CF039898
EST:     ACAAGAAGAATGAG                         GTTTTCTTGGACATAGTTGAGAGTGTAAACCTTCTTATGTCTTCGAAAG
genomic: ACAAGAAGAATGAGgtgcttaaac ... ttttcatcagGTTTTCTTGGACATAGTTGAGAGTGTAAACCTTCTTATGTCTTCGAAAG
EST: gi|211055145|gb|FL320202.1|FL320202
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|5525788|gb|AI861681.1|AI861681
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|31354959|gb|CD439316.1|CD439316
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG
EST: gi|76918953|gb|DV167527.1|DV167527
EST:     CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG        
genomic: GGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagG

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: 271

CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagGTTTTCTTGGACATAGTTGAGAGTGTAAACCTTCTTATGTCTTCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagGTTTTCTTGGACATAGTTGAGAGTGTAAACCTTCTTATGTCTTCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 381

CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagGTTTTCTTGGACATAGTTGAGAGTGTAAACCTTCTTATGTCTTCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 382

CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac ... ttttcatcagGTTTTCTTGGACATAGTTGAGAGTGTAAACCTTCTTATGTCTTCGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaactatacatgtgtacctctcgtcttatttgatcccattctttgcacttttgttcatctactagttgcactagtggagtaatctttttttcatcag

- - - - - - GCTGTT
- - - - - - - - - - TTGGAG
- - - - - - - - - -  TGGAGA
- - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - -  AAGAAG