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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaaaattactaacactgtactccagtgtgagctactactactagtactagctgatgagctgaccgtttgtgaatttgggttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAG

Basic information

species Oryza sativa
transcript LOC_Os09g31300.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g31300.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G085467_T02 (Zea mays), 3'ss of exon 3
------------------------------------aaaaaaaattactaacactgtactccagtgtgagctactactactagtacta-gctgatgagctgaccgtttgtgaatttgggttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAG------
                                      ||||  | ||  ||  | || |    | |   |  | |  | |   ||   ||     || | | | |||||   | | | |  ||||  |   ||||||||||||||||||| |||||| ||||||| |||||||||||||||||||| || |||||||||      
gtaaccaagacccaagaaagatcgatagacgaacagtgaaaacgtcac-gacgttttatttttattttcacc-caaagaatgcaacggcgcaagatagataaacttttgttgttgttgttgatggtgatggatgcagCAAACCAACACTGCCGACATGCTGGATCTGGCCGTGGACTACATCAAGGATCTTCAGAAGCAGGTCAAG

upper sequence: LOC_Os09g31300.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G417597_T02 (Zea mays), 3'ss of exon 1
------------------------------------------------aaaaaaaattactaacactgtactccagtgtgagctactactactagtactag--ctgatgagctgaccgtttgtgaat----------ttgggttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAG------
                                                |    |    | |  | ||   ||||| |      |  |||||| ||||| ||    ||  |||      ||  |  ||            || ||| | |  |   ||||||||||||||||||| |||||| ||||||| || ||||||||||||||||| || |||||||||      
gtaaccaaacccagcccaaaccccaagaaagatggatagaacagtgaaacgtcacgccattcccgctcacctccactcctgattggtactaccagtaccagaatagaacagcgagagattgatagataaactgacgaccggttttcgttgatggctgcagCAAACCAACACTGCCGACATGCTGGATCTGGCTGTGGACTACATCAAGGATCTTCAGAAGCAGGTCAAG

upper sequence: LOC_Os09g31300.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G51140.1 (Arabidopsis thaliana), 3'ss of exon 4
aaaaaaaattactaacactgtactccagtgtgagctactactactagtactagctgatgagctgaccgtttgtgaatttgg-gttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAG------
            | | | | |    |  | |      ||  || | |||||   | |||  ||   | |   || ||||    | ||   || |  |||||||||| ||||| || ||||||||||||||||| ||  | ||||||||||| || ||  | ||       
-----------gttagattatg---cgatcttcctctctcatattcgtact--ttcatgttctttgc-tcaatgtatttatcatcttcaattgatatgcagCAAACAAACACAGCAGACATGTTGGATCTTGCGGTTCAATACATCAAGGACCTGCAAGAACAAGTGAAG

upper sequence: LOC_Os09g31300.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g07810.t01 (Vitis vinifera), 3'ss of exon 4
aaaaaaaattactaacactgtactc-cagtgtgagctactactactagtactagctgatgagctgaccgtttgtgaatttgggttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAG------
  | ||  |   | | | | | ||| | |  ||    | |  |   | |  |  |   | | ||     ||  |   | ||  || |     |  | |||||||||||||||||| |||||||| ||| | |||||||| ||||| ||||| || ||||| |||      
gtagaatttctatgaaattttcctctctggttggataaattttttcaatgttt-caattcaacttctaattaatatctgtgaattct-----tcttggcagCAAACCAACACTGCAGACATGTTAGATTTGGCCGTGGAATACATTAAGGACCTTCAGAAACAGTACAAT

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|218488565|gb|FG946156.1|FG946156
EST:     TCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTCCCCAACATGGAAAAG                         CAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAG
genomic: TCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTCCCCAACATGGAAAAGgtgaggggga ... ttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAG
EST: gi|29669314|gb|CB665589.1|CB665589
EST:     TCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTCCCCAACATGGAAAAG                         CAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAG
genomic: TCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTCCCCAACATGGAAAAGgtgaggggga ... ttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAG
EST: gi|29657039|gb|CB653314.1|CB653314
EST:     TCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTCCCCAACATGGAAAAG                         CAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAG
genomic: TCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTCCCCAACATGGAAAAGgtgaggggga ... ttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAG
EST: gi|29669315|gb|CB665590.1|CB665590
EST:     TCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTCCCCAACATGGAAAAG                         CAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAG
genomic: TCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTCCCCAACATGGAAAAGgtgaggggga ... ttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtactagctgatgagctgaccgtttgtgaatttgggttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAG
              agctgac  putative branch site (score: 3)
                                           ttttactt  putative PPT
                                           ttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaaaattactaacactgtactccagtgtgagctactactactagtactagctgatgagctgaccgtttgtgaatttgggttttggttttacttgcagCAAACCAACACTGCTGACATGTTGGATCTTGCCGTGGACTACATCAAGGAGCTCCAGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
aaaaaaa
- - - - - actaaca
- - - - - - - - - - - - - - - - agctact
- - - - - - - - - - - - - - - - - - - - - - - - - - gctgatg