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'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcattctcaacttccttttcattgttgaagtacaggttatttcttatctgaattattgtgattgaactccacttgttacaatctgatgaattaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCGAAGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGC

Basic information

species Oryza sativa
transcript LOC_Os07g47530.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47530.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 14
agcattctcaacttcct-tttcattgttgaagtacaggttatttcttatctgaattattgtgattga-actccacttgttacaatctgatgaatt---aatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCGAAGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGC
     || ||     || | |  ||    || |  | ||| |   ||   ||     ||   |||   |  |    | |||| ||||| || |||   ||||||||||||||||||||||| |  ||| ||||| ||||| || || |||||  | |||||| | |||||||| ||||||||||||||||||||  || ||||  
-----tcccattgagctatcttgttaccaaatttaatgttttgattttaatgcgcccttacaattatcatgctgtattttacgatctgttgtattgtcaatgcagGATAGCTTTGGTCGGGCGGGTGAAAAAAATAAAGAAGCACTCAAGATGTCAAAGCATATAACTAAACTTTTCCCAAATAAAGTGACAATTGAATCACCTG
















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|33797016|gb|CF324371.1|CF324371
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|58692536|gb|CK081223.1|CK081223
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|58660071|gb|CK048751.1|CK048751
EST:     TCCTTTCAAAATTCCCATACAGNCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACACAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|29632741|gb|CB637750.1|CB637750
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTGTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTG
EST: gi|58690470|gb|CK079157.1|CK079157
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|58652949|gb|CK041629.1|CK041629
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|58690512|gb|CK079199.1|CK079199
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|33675839|gb|CF304078.1|CF304078
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|58658063|gb|CK046743.1|CK046743
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|33675419|gb|CF303658.1|CF303658
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|29685521|gb|CB681796.1|CB681796
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|58660377|gb|CK049057.1|CK049057
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
EST: gi|33676430|gb|CF304669.1|CF304669
EST:     TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAG                         GATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG
genomic: TCCTTTCAAAATTCCCATACAGCCAAGCAATACTCGACCTCACCTTCCAGgtgtgttttt ... attaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgaattattgtgattgaactccacttgttacaatctgatgaattaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCGAAGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGC
                                            aattaat  putative branch site (score: 3)
                                         atgaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcattctcaacttccttttcattgttgaagtacaggttatttcttatctgaattattgtgattgaactccacttgttacaatctgatgaattaatgcagGATAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCGAAGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGC

agcattc
- - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatga