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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaatctgccttggctccttcatagatactgatatggttctacattacaatgcaaagtatgatcgctaaattataaacgtgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTCACTTTAGCTGGCCTGACTGTTAGGAGTTACCGCTACTATGATCCTGCAA

Basic information

species Oryza sativa
transcript LOC_Os01g55540.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G094712_T02 (Zea mays), 3'ss of exon 5
gtaaggaatctgccttggctccttcatagatactgatatggttctacattacaatgcaaagtatgatcgctaaattataaacgtgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTCACTTTAGCTGGCCTGACTGTTAGGAGTTACCGCTACTATGATCCTGCAA
        |    |||  ||   || ||  |  |    || |||   |||| ||||||     |||  ||||||| ||| |  | |  ||||||||||||| ||||||||||| ||||||||||| |||||||| ||||| |||||  || ||||| |||  |||||||| |||||||| |||||||||||||
-------gttaaacttttcttgctcctatctgttttgctgcttcctgattataatgca-----tgactgctaaatcatacaaatatattccagCGCACTATCTACATCCCACAACCAACCTGGGGAAATCACCCAAAAGTCTTCACCCTATCTGGCTTGAACGTTAGGAGCTACCGCTATTATGATCCTGCAA
















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|32948428|gb|BP185000.1|BP185000
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|33685641|gb|CF313880.1|CF313880
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|44667509|gb|CR280943.1|CR280943
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|33678230|gb|CF306469.1|CF306469
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|218483847|gb|FG951547.1|FG951547
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|33794428|gb|CF323098.1|CF323098
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|425867|gb|D22545.1|D22545
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|58591056|gb|CF989364.1|CF989364
EST:     CTGGTTCTTTAAGGGTGGGAGGTGCATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCA
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCA
EST: gi|29639571|gb|CB644580.1|CB644580
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|27576897|gb|CA999591.1|CA999591
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|32948311|gb|BP184883.1|BP184883
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|218483959|gb|FG947666.1|FG947666
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|33793733|gb|CF322749.1|CF322749
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|33794958|gb|CF323359.1|CF323359
EST:     TGGTTCTTTAAGGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: TGGTTCTTTAAGGG-TGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|425866|gb|D22544.1|D22544
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|58656014|gb|CK044694.1|CK044694
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|29679665|gb|CB675940.1|CB675940
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|29660055|gb|CB656330.1|CB656330
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|163926589|gb|EG713605.1|EG713605
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|32948296|gb|BP184868.1|BP184868
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|2310086|gb|C26241.1|C26241
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|218478855|gb|FG949686.1|FG949686
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|29658837|gb|CB655112.1|CB655112
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|33680310|gb|CF308549.1|CF308549
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|33678676|gb|CF306915.1|CF306915
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|58694708|gb|CK083395.1|CK083395
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGG
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGG
EST: gi|33793380|gb|CF322571.1|CF322571
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|10794714|gb|AU108680.1|AU108680
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTTTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTNTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|33795088|gb|CF323417.1|CF323417
EST:     TGGTTCTTTAAGGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: TGGTTCTTTAAGGG-TGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
EST: gi|58669037|gb|CK057723.1|CK057723
EST:     CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTTCAAGGCATTATCATGAA                         CGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC
genomic: CTGGTTCTTTAAGGGTGGGAGGTGAATTTCTTGCAAGGCATTATCATGAAgtaaggaatc ... tgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttctacattacaatgcaaagtatgatcgctaaattataaacgtgttctccagCGCACTATATACATCCCACAGCCAACCTGGGGGAATCACCCCAAAGTGTTCACTTTAGCTGGCCTGACTGTTAGGAGTTACCGCTACTATGATCCTGCAA
                             cgctaaa  putative branch site (score: 3)
                                             tgttctcc  putative PPT
                                taaattataaacgt  TA-rich tract