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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatgtgaattttagatcttctttgaatttacttaaatgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatgttacag

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatgtgaattttagatcttctttgaatttacttaa-atgcatagatatcgattgtgtttgtagaaaacatgccagt--ttccctgttaccaatgaaaaattcaaacatgttacag
||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||| |||| || | |||||||  ||  |  | ||  || ||| | |||   || | |||  | |   ||      |  |  ||||||| ||                        
GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatttgaacttcatatcttctccgagctctcatatcattcattg-tattcttttttttttgacactgcaaaattataatctcctgttaacag-----------------------

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AC207890.3_FGT002 (Zea mays), 5'ss of exon 2
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatgtgaattttagatcttctttgaatttacttaa-atgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatgttacag
||||||||||||||||| || || || ||||| ||||||||||| |||||||||||||| || || ||||| ||||| || ||| |||| || | ||||||| | || |  | ||  || ||| | |||   |  | ||| | || ||  ||| |  ||      | |   |  |                   
GCTCGCCGTGGTGGAGTTGACGAGCCCTTTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAGgtgctacatttgaacttcatatcttctctaaactctcgtatcattcattg-tattcttcctttttttggacaa--tgcaaaattataatctgctgttacag------------------

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G38010.1 (Glycine max), 5'ss of exon 3
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg---tgaattttagatcttctttgaatttactta-----------aatgcatagatatcgattgtgt-ttgt-----agaaaacatgccagtt-tccctgttaccaatgaaaaattcaaacatgttacag-----
|| ||  | ||||| ||||| || || ||||| ||||||||||| |||||||| ||||| ||||||||||| ||||| |         |||| |  || || |   |  ||| | ||            | | | |   | | | || ||| ||||        || | ||| | || || ||| |   |  |  |  ||  ||  | ||   |     
GCGCGTAGAGGTGGTGTGGACGAGCCTTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgcgttgaaaattgaaatagagttcattggttgattcagttgctactactactactacttgagtgttggttttgtcttgtttctggtgaagcgtgcaatttgtctctgatgtgatgggtatgttggaaatttttttggaacag

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G17050.4 (Glycine max), 5'ss of exon 3
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg---tgaattttagatcttctttgaatttacttaaatgcatagatatcg--attgtgtttgtagaaaacatgccagtttc-cctgttaccaatgaaaaattcaaacatgttacag------------------------------------------
|| ||  | ||||| ||||| || || ||||| ||||||||||| |||||||| ||||| ||||||||||| ||||| |         |||| |  || || |   |  ||| | ||      |    || |   | | || |   |   |   ||   ||||   ||  |     |||||   |  ||  |||  | |                                          
GCGCGTAGAGGTGGTGTGGACGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgcgttgaaaattgaaatagagttcattgattgattcagttgctactactactaccactactttgatctgatcgagtgtggtggttttgtcttgttttggtgaaagcgtgcaatgtgtctctgatgtgatggttttgttgggattttattttttttttggaacag

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatgtgaattttagatcttctttgaatt-tacttaaatgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatgttacag
|||||| | || ||  | ||||| || ||||| |||||||||||||||||||||||||| || ||||| |||||||| ||   | | || | |  |||   | ||  || ||  | |  | || || |    || | ||  ||  ||   |   |   |   | ||  |  |||  |                 
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaa--agttttcttcatattaacagtttaaaccttttttttttct-tgagcag----------------

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 5'ss of exon 2
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatgtgaattttagatcttctttgaatttacttaaatgcatagatatcgattgtgt-ttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatgttacag
|| ||  | |||||  | |||||||||||||| ||||| || || |||| | | ||||||||||||||||||||||| |  |   |  |  ||   |    |||    | |    |||       | |  |   ||  |  |     ||      |||    | ||    |  | |                  
GCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAGgtgcctctcatacaacttttcttccttttatggtgatcctaatattctcttttgaaccatgaatcctgtcttactcagatgttgttgtattgattacaatag-----------------

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|88328058|gb|CI649856.1|CI649856
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCANATTC
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTC
EST: gi|29687922|gb|CB684197.1|CB684197
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|29631511|gb|CB636520.1|CB636520
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|29622580|gb|CB627591.1|CB627591
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|29636331|gb|CB641340.1|CB641340
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|88367108|gb|CI563872.1|CI563872
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|88361419|gb|CI605200.1|CI605200
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAGAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|6012905|gb|AU078722.1|AU078722
EST:     ATTTGCTTGGGAAAGCAGGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: ATTTGCTTGGGAAAGCAGGG-AGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|29627292|gb|CB632303.1|CB632303
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|117240306|gb|CT842733.1|CT842733
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
EST: gi|58680371|gb|CK069058.1|CK069058
EST:     CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG                         GAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT
genomic: CATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatg ... catgttacagGAGGTCACATTCAGAGTGGACTACACAGCTCCAAATGTTGGACGAGAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatgtgaattttagatcttctttgaatttacttaaatgcatagatatcgattgtgtttgtagaaaacatgccagtttccctgttaccaatgaaaaattcaaacatgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA