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

CTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgtggacttcaaagttcagattgtttgctcacacttctctttcaattacagtaaaagcaatgatcatttctttgcatctatctttagctgctg...

Basic information

species Zea mays
transcript GRMZM2G065757_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065757_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 4
CTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaag-ctcgtggacttcaaagttcagattgtttgctcacacttctctttcaattacagtaaaagcaatgatcatttctttgcatctatctttagctgctg---
|||| ||||||||||| ||||| ||||||||||||||||||||||||||||||||||| || ||||| ||||| || |||||  |||||  ||| |||||||||| |     |||||    | ||  | | |||| |  |   || || |   | |||||| |||  | | |   |  ||||||| ||    |      ||   
CTACCAAGGAGCCAGGTCTTACTTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTTGGATTTCAGGAAATATCCGTTGGAGATGCAGTACCTGTGTGgtaagacaacctgacttacgtgatctaagtttttgatttc---tcactgtggttcacagtagaagagaaggt-gctcttttgcatatagtgattatatttgtat
















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|149095835|gb|EE181486.2|EE181486
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
EST: gi|149078470|gb|EE167250.2|EE167250
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
EST: gi|32830382|gb|CD970060.1|CD970060
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCGTTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
EST: gi|32840007|gb|CD979688.1|CD979688
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACGAGGTCTCATCAGCGACCCTGTTTTCTCGGTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
EST: gi|32850768|gb|CD990449.1|CD990449
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCGTTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
EST: gi|50338072|gb|CO533198.1|CO533198
EST:     TTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAAATGCA-CACCAGTGTG                         GTATAACATGGTGAAACAAGGT
genomic: TTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAA-TGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGT
EST: gi|32839505|gb|CD979186.1|CD979186
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTTCTCGTTTC
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTT-CTC-TTTC
EST: gi|33097906|gb|CF057866.1|CF057866
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACCAAGGTCTCATCAGCGACCCTGTTTTCTCGTTCT
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAA-CAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCT
EST: gi|148956524|gb|EC902364.2|EC902364
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
EST: gi|148931369|gb|EC874278.2|EC874278
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
EST: gi|211224724|gb|FL222442.1|FL222442
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG
EST: gi|33099258|gb|CF059218.1|CF059218
EST:     CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTG                         GTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCGTTCTG
genomic: CTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgt ... aaaattgcagGTATAACATGGTGAAACAAGGTCTCATCAGCGACCCTGTTTTCTCTTTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACAAAGGAGCCAGGGCTTACCTTCATGGTTGCAAAATTTGATGGCATTCTTGGGCTAGGCTTTCAAGAAATCTCTGTTGGGAATGCAACACCAGTGTGgtaagctcgtggacttcaaagttcagattgtttgctcacacttctctttcaattacagtaaaagcaatgatcatttctttgcatctatctttagctgctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagcaa