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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgcatgatgttcctttttacttcttttgtaacacaccgaaatttgtactgacatatcaattatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAAGACTTAAATGTCTCCTGGAAGAAGAATGGACAGTACAACATGAAATGCA

Basic information

species Oryza sativa
transcript LOC_Os03g17980.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 8
gttttgcatgatgttcctttttacttcttttgtaacacaccgaaatttgtactgacatatcaattatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAAGACTTAAATGTCTCCTGGAAGAAGAATGGACAGTACAACATGAAATGCA
|| ||| ||  ||||| ||||   ||  ||||||   | |    | ||||| |||  ||||| ||| ||||||||| || || || ||||| || |||||| |||||||| |||| ||||||||||| ||||| |||   |||||||||||||| || |||||| |||||||||
gtattggatactgttcattttactttactttgtatggc-ctagcacttgtattgatgtatcacttaaccaacagTCTCGGGCCCACCCTCGTGAAATAATGGTTGAGGTCTTAAAAGCACTTCAAGAATTAAACGTCAGATGGAAGAAGAATGGGCACTACAACGTGAAATGCA

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 9
---------------gttttgcatgatgttccttt-------ttacttcttttgtaacacaccgaaatttgtac-tgacatatcaattatcc---aacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAAGACTTAAATGTCTCCTGGAAGAAGAATGGACAGTACAACATGAAATGCA
                ||||| |  |  | || |        ||     |||  |  |     |  | || ||       | |  ||||||     |||||| ||||| || ||||| || ||||||| ||||||||| || ||  | ||||| |||||||| |  |||||||||| ||| || ||||||||||| || |
taacggctgtttgaatttttgtaatagttgccatcagaaaaattgtagttttgatgtcttgttggtagttatatactttttgttcattatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA
















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|86492611|gb|CI135244.1|CI135244
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|89186738|gb|CI052151.1|CI052151
EST:     ATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: ATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|38477992|gb|CF962125.1|CF962125
EST:     TTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGTGACTTCAG                         TCAGGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAACAGGCACTTC
genomic: TTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTG-GACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAA-AGGCACTTC
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|5038573|gb|AU070683.1|AU070683
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|38483178|gb|CF966980.1|CF966980
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTC-TGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|2317410|gb|C22464.1|C22464
EST:     CCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: CCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|218478287|gb|FG959067.1|FG959067
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|218493226|gb|FG956765.1|FG956765
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|66915430|gb|CX102278.1|CX102278
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAGCCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|218504457|gb|FG953019.1|FG953019
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|11025963|gb|AU162564.1|AU162564
EST:     TTTNCGCCCACATTANCCTGTTGAAANGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCACCCTCGCGAGATAATGATTGAGGTCCTAAAGNCACTTCAA
genomic: TTTGCGCCCACATTATCCTGTTGAAA-GAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
EST: gi|29672696|gb|CB668971.1|CB668971
EST:     GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAG                         TCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA
genomic: GTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttttgcatg ... tatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacttcttttgtaacacaccgaaatttgtactgacatatcaattatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAAGACTTAAATGTCTCCTGGAAGAAGAATGGACAGTACAACATGAAATGCA
                              tactgac  putative branch site (score: 1)
                                     atatcaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgcatgatgttcctttttacttcttttgtaacacaccgaaatttgtactgacatatcaattatccaacagTCACGAGCTCAACCTCGCGAGATAATGATTGAGGTCCTAAAGGCACTTCAAGACTTAAATGTCTCCTGGAAGAAGAATGGACAGTACAACATGAAATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG