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

CGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactctactttcccagttggtttacttctgcaaattatctgcatcaataatatttgcctacagtataagatcgggtggtggttatgccacattgca...

Basic information

species Zea mays
transcript GRMZM2G375904_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g43570.3 (Oryza sativa), 5'ss of exon 10
CGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactctac--tttcccagttggtttacttctgcaaattatctgcatcaataatatttgcctacagtataagatcgggtggtggttatgccacattgca
  ||||| | |  ||||| |  ||||||||||||||||||||||||||||||||||||||  | |||||||||||||||||||||||||| || ||||||||||   ||     ||| ||  ||||| |  |||     || || || |  |   || |      ||  | |   ||  ||| ||| |  |   || |||| 
TAGAGGTCTCCCATGGGAAAGATTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAACAGCGAGTTGGATACTCAGAATTTTGAGAAATTTGAGGAGgtaaatttcagtcgttttcccattggtctgattcatgtgataatttg-aggagggatttcgtttcaccttgttttattaggttgtgatcttaa-accttgct

upper sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 5'ss of exon 9
CGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgt-aatactc-tactttcccagttggtttacttctgcaaattatctgcatcaataatatttgcctacagtataagatcgggtggtggttatgccacattgca
|  |||  | |  ||||| | ||| ||| | ||| | || ||||| | ||| ||||| || |  |||||||||||||||||||||||||| || || ||||| || | || | | |  | ||    ||   ||         ||| | |||  |   | |     |     |||  || | || |  || |   | | |   
CAAAGGATTGCCATGGGAAAGGTTATATGAAATGGAGGCCGCTTTTAAACCGGAAGTGAAAGATGAGTTGGATACTCAGAATTTTGAGAAATTTGAAGAGgttaacagtccttcctatctagaacattcgtttacctttcaaatcagaatctttggcactcttagagttgttaaactctgatgataattttcaaatagtt--

upper sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 5'ss of exon 9
CGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgt-----aatactctacttt--cccagttggtttacttctgcaaattatctgcatcaataatatttgcctacagtataagatcgggtggtggttatgccacattgca
|   ||  | |  ||||| ||| ||||| | ||| | || ||||| | ||| || || || |  ||| |||||||||||||||||||||| ||||| |||||     |  | ||   |    || | | | ||  |||   ||     |  |  |   | ||| | | ||| | | |  |  | | ||     |    |||||    
CCATGGATTGCCTTGGGATAAGCTGTATGATATGGAGGCAGCTTTTAAACCCGAGGTGAAAGATGAGCTGGATACTCAGAATTTTGAGAAGTTCGAAGAGgtttaccatcattcctgtccaacctaatcgattatcttacacatggcctaggggtatctgatactggtctagattgtgcgcaccgatgtctact----cacatc---

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|5895617|gb|AW036863.1|AW036863
EST:     CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
EST: gi|28187719|gb|CB179329.1|CB179329
EST:     CAGAAGTTAATGGAGAGTTGAATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
EST: gi|5901099|gb|AW042199.1|AW042199
EST:     CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
EST: gi|33285627|gb|CF075422.1|CF075422
EST:     CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
EST: gi|211195854|gb|FL001022.1|FL001022
EST:     CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
EST: gi|31628455|gb|CD526616.1|CD526616
EST:     CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGA
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGA
EST: gi|149049839|gb|EE048526.2|EE048526
EST:     CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
EST: gi|32870336|gb|CF010018.1|CF010018
EST:     CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
EST: gi|32928081|gb|CF032893.1|CF032893
EST:     CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAG                         ATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG
genomic: CAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactct ... tactttgcagATTGGAACTCAAATTCAAAGTTCATCCAAGTCAGGCCCTTGGAGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGAGGTGTTCAGTGGGAGAAGTTGTATCAGATGAAAGCTGCTTTCATACCAGAAGTTAATGGAGAGTTGGATACTCAGAATTTTGAGAATTTCGAGGAGgtaatactctactttcccagttggtttacttctgcaaattatctgcatcaataatatttgcctacagtataagatcgggtggtggttatgccacattgca

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG