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

gtaaggtgttttgggggaatttctattgattttttgctccttcgtattttggattggattggtggtggatttgacttcgattttgtggtctgatcggagtaggaagggaagCCCCTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 2
gtaaggtgttttgggggaatttctattgattttttg----ctccttcgtattttgg---attggattggtggtggatttgac-ttcgattttgtggtctgatcggagtaggaagggaagCCCCTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC
||||| ||  || ||||| || ||||  |  || |     | | |  || ||||      ||||||||| | ||||||||||  ||   ||  |  |||||||   | |||||||||||||||| |||||||| |||||||||||||| ||||| ||| ||||||| || ||
gtaagatgagtttggggatttgctatgaaccttctaattccccttctgtttttttattagttggattggagatggatttgacgctcctgttcctattctgatctctgcagGAAGGGAAGCCCCTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCC

upper sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G094712_T05 (Zea mays), 3'ss of exon 2
gtaaggtgttttgggggaatttctattgattttttg----ctccttcgtattttgg---attggattggtggtggatttgac-ttcgattttgtggtctgatcggagtaggaagggaagCCCCTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC--------------------------------------
||||| ||  || ||||| || ||||  |  || |     | | |  || ||||      ||||||||| | ||||||||||  ||   ||  |  |||||||   | |||||||||||||||| |||||||| |||||||||||||| ||||| ||| ||||||| || ||                                      
gtaagatgagtttggggatttgctatgaaccttctaattccccttctgtttttttattagttggattggagatggatttgacgctcctgttcctattctgatctctgcagGAAGGGAAGCCCCTAGTGCTGAACGTGGTCAGGCGCGCCGAGCAAATGTTGATCAATAATCCGTAAGTGTCATGTGAAATCCATATGACCCGCTTGATTT
















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:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|33685641|gb|CF313880.1|CF313880
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|44667509|gb|CR280943.1|CR280943
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|58591056|gb|CF989364.1|CF989364
EST:     ATCCCAGTCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         CCCCTGGTGCTGAATGTGGGCAGGCGCGCTGAGCAGATGCTGATCAACAAC
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaagCCCCTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAAC
EST: gi|29639571|gb|CB644580.1|CB644580
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|32948311|gb|BP184883.1|BP184883
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|218483959|gb|FG947666.1|FG947666
EST:     GCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: GCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|33794958|gb|CF323359.1|CF323359
EST:     GTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: GTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|58656014|gb|CK044694.1|CK044694
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|29679665|gb|CB675940.1|CB675940
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|29660055|gb|CB656330.1|CB656330
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|32948296|gb|BP184868.1|BP184868
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|218478855|gb|FG949686.1|FG949686
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|10931116|gb|AU161390.1|AU161390
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|29658837|gb|CB655112.1|CB655112
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|58694708|gb|CK083395.1|CK083395
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|218490932|gb|FG946901.1|FG946901
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|8527391|gb|AU092206.1|AU092206
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAG                         G
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGgtaaggtgtt ... ggaagggaag-
EST: gi|33793380|gb|CF322571.1|CF322571
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|33795088|gb|CF323417.1|CF323417
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg
EST: gi|58669037|gb|CK057723.1|CK057723
EST:     ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACCGAGGAAGGGAAG                 
genomic: ATCCCAGCCCCGTGAAGGTCAATCTCGGCGTCGGCGCCTACCGGACC--------G-AGgtaaggtgtt ... gg


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggtggtggatttgacttcgattttgtggtctgatcggagtaggaagggaagCCCCTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC
                               gtctgat  putative branch site (score: 4)
                       attttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtgttttgggggaatttctattgattttttgctccttcgtattttggattggattggtggtggatttgacttcgattttgtggtctgatcggagtaggaagggaagCCCCTGGTGCTGAATGTGGTCAGGCGCGCTGAGCAGATGCTGATCAACAACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT