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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC

Basic information

species Oryza sativa
transcript LOC_Os08g25734.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 3
gtatgcaaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcag--ttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC
                  | | | |     |  |  |  | ||||     || |     || || ||    |  | |  | ||  |  | |||  | |||  | |||   |  ||||||||||||| ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||  | || ||| ||||||||||||
-----------------ttctataggattttaatccttcaaagttcctccattttttctttgttccaaaggagcccttaaaatgcattcacatcatattgt-tgtttgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATCTATGTTTTCAGCAAAGATGTAATGCTTC

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 3
gtatgcaaatgacgtgcctttcttgctaacttg---tgatatacagttgtgagatatcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtct------tgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC
   | || || |  |||||||  |   ||  |    ||| ||||| ||||     |||| ||| |  |||  | |  | |   |  ||| |   ||  |  | |||||  ||||      ||||||||||||| ||||||||||||||||| |||| ||||||||| ||||||||||||||||||||||||||||| |||||  |||| ||  ||||||||||||
--gtacacataatttgccttttctttcaagctaacttgacatacatttgttgacaatcatttagtgaacctaaaatattcccctttaaaatgccttcatctcatatttctgtctgattgatgtagGTTGACACCACCATACTTGGCCTTGATGACGAGAGGGCAAAGGAAATGCCTTATATTGCTAGCATGGGTATATATGTTTTTAGCAAGGATGTAATGCTTC

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G061795_T01 (Zea mays), 3'ss of exon 4
--gtatgcaaatgacgtgcctt-tcttgctaacttgtgatatacagttgtgagatatcagttattacaccaca-tacttccatatcaaaactcattttgttgcctattttcgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC
  |   ||||| |   ||| || | |||||| | || |||||    ||||       ||  | | |  |  ||   | |||||    ||  || |   |      | ||| |   || |||||           |    || |||   |   |||||                                                               
gtgagggcaaaggcaatgctttatattgctagcatg-gatatct--ttgtttttagCCAAGTGTAATGCTTCAGCTCCTCCATGAACAATTTCCTGGAGCCAATGACTTTGGAAGTG-AGGTTATTCTAGGTGCAACCAGCATTGGAAA---GAGGGTTC------------------------------------------------------------

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 3
gtatgcaaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC
                                    ||  |   | | | || |    |||      |  ||  |  | || |  ||        |||| ||     | |   |||||||| ||||| ||  | || ||||| |||| ||| ||||| ||| ||||||||||||||||||||||||| |||||  |||| ||||| || ||| |  
-----------------------------------gtaagcccatataacatgtattatatgttgttatttatctggaaattattacctgagcaattgcttaaaaatgccac-tagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCTTATATTGCTAGCATGGGTATATATGTTGTTAGCAAAAACGTGATGTTAG

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 3
gtatgcaaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatat-cagttattacaccacatacttccatatcaaaactcattttgttgc-ctattttcgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC
                        || | |     ||||| || |||   ||||   ||||||   |   | | |   |  | || | |   ||       | | |||  | || |||||||| ||||| ||  | || ||||| |||| ||| ||||||||||||||||||||||||||||||||||| |||||  |||| |||||||| ||| |  
------------------------gcaagccc---atata-agatgtattatatgttgttatttatctggaaattattacctgaacaattgcttaaaaatgccacttttcttttctagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATATATGTTGTTAGCAAAAATGTGATGTTAG

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 3
--gtatg-caaatgacgtgc-ctttcttgctaacttgtgatatacagttgtgagatat--cagttattacaccacatacttccatatcaaaact----cattttgttgcct--attttcgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC
    |||  |  |||  |   | ||| |  ||| || || | |   |||     ||    || || |        | | ||   ||  ||  ||    | ||||  |  ||  | | |    ||  |||| || |||||||| || || ||||| || | ||| || |||||||||||||| |||||||| |||||||| |||||  | || ||| |||| ||| |  
gtagatgatatttgaaataaacattcgtattaatttatgcttttgtgttcctctattctacaattttgtagttttaaagttggttaagaaggctgatacgttttcctttctgaactgttccttttaagGTCGATACTACCATCCTGGGTCTTGATGATGAGAGAGCTAAAGAAATGCCTTACATTGCTAGTATGGGTATATATGTCGTCAGCAAAGATGTGATGTTAG

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|13420424|gb|AU174514.1|AU174514
EST:     GAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGANATGCCT
genomic: GAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|87012877|gb|CI297104.1|CI297104
EST:     GAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: GAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|33681770|gb|CF310009.1|CF310009
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|58678083|gb|CK066770.1|CK066770
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|88586416|gb|CI704115.1|CI704115
EST:     ATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: ATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|29614233|gb|CB619246.1|CB619246
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|58652879|gb|CK041559.1|CK041559
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAGCAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|58675386|gb|CK064073.1|CK064073
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|29681248|gb|CB677523.1|CB677523
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|88584775|gb|CI702352.1|CI702352
EST:     ATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
genomic: ATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT
EST: gi|58668409|gb|CK057095.1|CK057095
EST:     TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATG                         GTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAGGAAATGCCT
genomic: TAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgcaaat ... cgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtagGTTGACACTACCATACTTGGCCTTGACGACGTGAGGGCAAAAGAAATGCCTTATATTGCTAGCATGGGTATCTATGTGATTAGTAAAAATGTAATGCTTC
                                     cctattttcgtctt  CT-rich tract
                atatcaaaa  TA-rich tract