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

gtatgttcactaccacatccacaaacttcataagcagttcttgttcagtctgtagatttaactgctagtgtacctaatgttgggcaattttatgtcctcggtgccactcatcgtaattttactgccaatttttgttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGGTGTCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATA

Basic information

species Zea mays
transcript GRMZM2G119725_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119725_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 2
gtatgttcactaccacatccacaaact-tcataagcagttcttgttcagtctgtagatttaactgctagtgtacct------------------aatgttgggcaa-------ttttatgtcctcggtgcc-------actcatcgtaattttactgccaatttttgttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGGTGTCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATA
||| |||   |||  || | ||    | |  | | | |||  | ||| || | |||   | | || || | || ||                  ||       |||       |||| | ||  ||||||         | ||| ||||||| | ||  ||  ||  | || ||||||| ||||||||| |||||||| ||| |||||||||| ||||||||||| ||||| ||| |||| ||| |||||||| | |||||||||||||| || |||
gtaggtttgatactgcagctactgtttattcttaactgtttcttttccgtttctagcgctgattgataatttatctgttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA

upper sequence: GRMZM2G119725_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g19510.3 (Oryza sativa), 3'ss of exon 1
gtatgttcactaccacatccacaaacttcataagcagttcttgttcagtctgtagatttaactgctagtgtacctaatgttgggcaattttatgtcctcggtgccactcatcgtaattttactgccaatttttgttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGGTGTCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATA
                                     | |    |      |||     |||    ||||| | |  | ||      | |   || |||   |   | ||| ||||||| | ||  ||  ||  | || ||||||| ||||||||| |||||||| ||| |||||||||| ||||||||||| ||||| ||| |||| ||| |||||||| | |||||||||||||| || |||
------------------------------------ttgcccacttgtctagtaacaccaacca--agtgttctttttctt------tctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
















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|148930418|gb|EE284901.2|EE284901
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|149108358|gb|EE292696.2|EE292696
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211020902|gb|FL324490.1|FL324490
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|76930436|gb|DV172388.1|DV172388
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|148937093|gb|EC881269.2|EC881269
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211226340|gb|FL315376.1|FL315376
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGC
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGC
EST: gi|211485903|gb|FL317494.1|FL317494
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCG
EST: gi|211457499|gb|FL333172.1|FL333172
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGNTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211404454|gb|FL338957.1|FL338957
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211017912|gb|FL318017.1|FL318017
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGC-TCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211220721|gb|FL343735.1|FL343735
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|148961302|gb|EE012027.2|EE012027
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211391716|gb|FL351031.1|FL351031
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211354854|gb|FL354353.1|FL354353
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211107153|gb|FL361596.1|FL361596
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|211160210|gb|FL316342.1|FL316342
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
EST: gi|149104738|gb|EE290190.2|EE290190
EST:     AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAG                         CATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG
genomic: AGAACTTCTGCAGTTCCTATGGCAAAGCCTCTCAATGGCAGTGGCCGTAGgtatgttcac ... ttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgtcctcggtgccactcatcgtaattttactgccaatttttgttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGGTGTCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATA
                                       tttttgtt  CT-rich tract
                                     aatttttgttattaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcactaccacatccacaaacttcataagcagttcttgttcagtctgtagatttaactgctagtgtacctaatgttgggcaattttatgtcctcggtgccactcatcgtaattttactgccaatttttgttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGGTGTCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG