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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatctaggatatttttcattgcctcatatctctttcaattgtgaaattatttcaagatgaatttctgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g52840.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G135283_T03 (Zea mays), 3'ss of exon 7
attatctaggatatttttcattgcctcatatctctttcaattgtgaaattatttcaagatgaatttc--------------tgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG
            |||| ||| ||  |||| |||||||  || || ||  |||||  ||||||||  |              | ||   |||||| ||||||||| | || | || |||||||||| || |||||||||||||||||||||||| |||| ||||||||||||||||| || || ||||| |||||||| |||||||||
------------atttgtcactg--tcatttctctttgtatggtaaacatattttgagatgaatcacactaacaccttactttctcctatgcttcatttgctacctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 7
attatctaggatatttttcattgcctcatatctctttcaattgtgaaattatttcaagatgaatttc--------------tgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG-------
            |||| ||| ||  |||| |||||||  || || ||  |||||  ||||||||  |              | ||   |||||| ||||||||| | || | || |||||||||| || |||||||||||||||||||||||| |||| ||||||||||||||||| || || ||||| |||||||| |||||||||       
------------atttgtcactg--tcatttctctttgtatggtaaacatattttgagatgaatcacactaacaccttactttctcctatgcttcatttgctacctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAGGCAAGGT

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 7
-attatctaggatatttttcattgcctcatatctctttcaattgtgaaattatttcaagatgaatttctgctgacat-gcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG
  | ||   || |    ||||     |   |  ||   |  |  || |  || |    | |||   | | ||   || |||||| ||  |   | | | ||| ||||||||||||| |  |||||||||||||| || || ||||| ||||| ||||| ||||| || |||||||| ||||  ||  | || |||
tgtgatgaggggttagattcacactttgcaaagtccccctttcatgca--tactgttggttgagactttcctataattgcttgacttatttaatatccgcagTTGGAGAAAAGTGCAGCACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7
----attatctaggat-atttttcattgcctcatatctctttcaattgtgaaattatttcaagatgaatttctgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG
    |     |||  | |   ||  ||||    |  | ||||||    |    ||  || |   ||   ||||  | | | |||||| ||  |   | | | ||| ||||||||||||| || |||||||||||||| || || ||||| ||||| ||||| ||||| || |||||||| ||||  ||  | || |||
gatgaggggttagattcacacttatttgcaaagtccccctttcatgcatactgttggttgagactg---ttcta-taata-gcttgacttatttaatattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 7
attatctaggatatttttcattgcctcatatctctttcaattgtgaaattatttcaagatgaatttctgc-tgaca-tgcttgatttgctacttctg---cacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG
                 |  ||  ||| | | |    ||||  |  | | | ||  |  | |    || | | ||| | | | | |   || || ||     |||||||||||||||||   |||||| |||||||| ||||| ||||| ||||||||||| |||||  |  | |||||||||| ||||||  | |||
----------------gttcttaactcttctattaagcaatcat--agtaacttataactaacccgcttcataacaatacataagtctttaattttgatttgcagATGGAGAAAAGTGCTACTCTTTTCAGGCCAAAATTGATTGTTGCTGGTGCAAGTGCTTATGCTAGATTGTATGACTATGCCCGCATCAGAAAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------------------------------------------------attatctaggatatttttcattgcctcatatctctttcaattgtgaaattatttcaagatgaatttctgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG
                                                                              | ||  ||  |   ||||| ||  |   | |    || | |  |  ||   |||  | |  ||  | |  | |  ||  ||||    || ||     ||| | || || |||||||| ||||| || || ||  | || ||||||||||||||||| ||||| ||||| ||||||||||  || || || |||
gttggttagttcatagccagcttagcttaatgcttcaacattctatctttatccaatataccattgagatatgggtttaatacatacaa-gcttttcgtttacggttcttatgttaagtaattgaacagtttttaaaccaaagtttatttatttg--tgatacaataattt---gcagCTAGAAAAGAGTGCCGTGCTTTTCAGACCGAAACTTATTGTTGCGGGTGCAAGTGCTTATGCTCGTCTATATGACTATGCACGTATTCGTAAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------------attatctaggatatttttcattgcc-tcatatctctttcaattgtgaaattatttcaagat---gaatttctgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG
                                                                                            | || | |   ||| ||  | ||  | ||  ||||     |  | ||  |   |  |  |   || | |    | ||| | |  |||||  | ||     |||||||||||||| || |||||||  |||||||| ||||| || || ||||| ||||| ||||| || | ||| |||||||  || ||||| |||
gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaaca-gatcaatttggaaattt---gcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG

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|29674139|gb|CB670414.1|CB670414
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|38472219|gb|CF956350.1|CF956350
EST:     CAATGCCCTACAGATAGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|27576793|gb|CA999487.1|CA999487
EST:     TGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATTGTTGCGGGTGCA
genomic: TGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|58691585|gb|CK080272.1|CK080272
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|29672938|gb|CB669213.1|CB669213
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|25798315|gb|CA754276.1|CA754276
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|38472528|gb|CF956660.1|CF956660
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGGCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|58661735|gb|CK050415.1|CK050415
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|58589569|gb|CF987877.1|CF987877
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAACAGTTGATCGTTGCGGGTGC
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAA-AGTTGATCGTTGCGGGTGC
EST: gi|29629705|gb|CB634714.1|CB634714
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAACCGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|84117692|gb|CD285458.1|CD285458
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|38471655|gb|CF955786.1|CF955786
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|33800499|gb|CF326119.1|CF326119
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|58689542|gb|CK078229.1|CK078229
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|58692794|gb|CK081481.1|CK081481
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|58609394|gb|CK037427.1|CK037427
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG                         ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA
genomic: CAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtc ... ttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattatttcaagatgaatttctgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG
                                         ctacttct  CT-rich tract
             atgaattt  TA-rich tract