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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGGAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaacattacagccttctaaagtttttattcagggatctagatgtaatctttttatctctttctgctgttag

Basic information

species Oryza sativa
transcript LOC_Os07g47290.3
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G081682_T01 (Zea mays), 5'ss of exon 18
GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGGAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa---cattacagccttctaaagttttt--attcagggatctagatg-taatctttttatctctttctgctgttag
| ||||||| |||||||||||||||||||||||||| || ||||| || |||||||||||||| || || ||||| || || |||| ||||||||| | |||||||||||   |||||   ||  || || ||||   || ||| | | |  |   |    ||||| |   | | || ||||||
GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGGgtaactggaaacacattaagacccactgaacttttcccatgcagaggtttttaaactggaatttttgt---tctgtgatgttag

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 18
GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGGAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaa----ctggaacattacagccttctaaagtttttattcagggatctagatgtaatctttttat------------ctctttctgc--tgttag
| ||||||| || ||||||||||||||| ||||||| |||||||| || |||||||||||||| ||||| ||||| || || |  | |||||||||||||||||    |  ||||| |   |    ||   ||  || |||       | | | |  | | | | |             |  |||||   ||||||
GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccgagaacaatcatgagacctgccgtactttttcgcatgctttgtttttttttgtgtgtaaagctggaagttttgttctgtgatgttag
















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|15854754|gb|BI807566.1|BI807566
EST:     GAATGGACACCCTAGCCC-CGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88974071|gb|CI002733.1|CI002733
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|89179716|gb|CI043995.1|CI043995
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|38476165|gb|CF960298.1|CF960298
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGNGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAG
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTG-GATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAG
EST: gi|89194258|gb|CI116695.1|CI116695
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88828748|gb|CI073618.1|CI073618
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88514668|gb|CI442174.1|CI442174
EST:     AAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: AAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|29688817|gb|CB685092.1|CB685092
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGAGGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|163927225|gb|EG710263.1|EG710263
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88985909|gb|CI033238.1|CI033238
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88506732|gb|CI434238.1|CI434238
EST:     CCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: CCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|218483389|gb|FG947207.1|FG947207
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88840977|gb|CI000939.1|CI000939
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCTCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|58031342|gb|CX728885.1|CX728885
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGAGGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88537783|gb|CI466758.1|CI466758
EST:     AATGGACACCCTAGCCCGCGGCCTTCGGAATGTTTTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: AATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88475673|gb|CI412944.1|CI412944
EST:     AGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: AGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88995441|gb|CI022764.1|CI022764
EST:     GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|313080767|gb|HO213564.1|HO213564
EST:     CCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: CCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
EST: gi|88504210|gb|CI431716.1|CI431716
EST:     GGACACCCTAGCCCNCGGCCTTCGGAATGTTGTCAAGCTGATCGAG                         GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT
genomic: GGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaa ... ctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGGAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAGgtaactggaacattacagccttctaaagtttttattcagggatctagatgtaatctttttatctctttctgctgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT