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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtacttaaatttatctagaatacttattctcaaaattttagttttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG

Basic information

species Oryza sativa
transcript LOC_Os03g52840.2
intron # 5
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 5
lower sequence: GRMZM2G135283_T03 (Zea mays), 3'ss of exon 5
-ttgtacttaaattta--tctagaatac-ttattctcaaaattttagttttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
    || |||  |||   |   ||  |  ||  ||||| ||| |||| |  ||||   | ||||  |    |  |||||    | | | |||| |||| |  ||||||||||||||||||||| || || || |||||||||||||| |||||||| || ||||| |||||||| || ||||||||||||||||||||||| ||
tcaatatttatcttttgtttctgaccatatttctctcataatgttagatgccttttcaccaaaattt----tcttaactcatgaccaattttcaacctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G36280.2 (Glycine max), 3'ss of exon 5
ttgtacttaaatttatctagaatacttattctcaaaattttagttttcttt-ctccaaaaaggtggcattctaacttgacaaccaatttctacctct--gcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
  || | ||  | | | |  | || ||     || |  ||  |    |     |   | || |||   |  |       |      | ||| | | |   |||| ||||||||| |  |||| || || ||| | |||||||| |||||||||||  |||||||||| ||||||||||| |||||  | |||||||| |||||
--gttcatatgtct-tttctattattttcctccacagcttgggggaacaaaattttgataatgtgctttcttggagaatcttatgttctctgcattttgacagTCAATGTGCAATCATTATCTGGATCCCCTTCTAACTTCCAAGTTTACACTGCTTTATTGAAACCTCATGAGAGAATTATGGCACTTGATCTTCCCCATGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 5
---------ttgtacttaaatttatctagaatacttattctcaaaattttagttttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
             | ||   || || |  ||||  |    | ||| | |||| | | | | |           |  |||| |  || ||        |      ||||||||| ||||| ||||| |||||||| ||||| || ||||| |||||||||||  |  | ||||| ||||| |||||||||||  | ||||||||||||||
ataatcactgaagagttttcttgatgttcaatagatccattaaaagtattaggtgtttgttt---------aagtcttctgatatgtcactgttaccccttaattgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCACGTTTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 6
--ttgtacttaaatttatctagaatactt---attctcaaaatttt--agttttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
  |        |  || |  |   | ||    ||||   |||||||  | |    ||| |||||       |  |||| |  || ||        |      ||||||||| ||||| ||||| |||||||| ||||| || |||||||| ||||||||  |  | ||||| ||||| |||||||||||  | ||||||||||||||
aatcacttaagagctttttcaatgtcctatagattcattaaattttgaaataaattttgtccaa-------gtcttctgatatgccactgttaccccttaattgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 5
ttgtacttaaatttatctagaatacttattctcaaaattttagttttcttt-ctccaaaaaggtggcattctaacttgacaaccaatttctacctct--gcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
  || | ||  | | | |  | || ||     || || ||  |    |     |   | || |||   |  |       |      | ||| | | |   |||| ||||||||| |  |||| || || ||| | |||||||| |||||||||||  |||||||||| ||||||||||| |||||  | |||||||| |||||
--gttcatatgtct-tttctattattttcctccacaacttgggggaacaaaattttgagaatgtgctttcttggagaatcttatgttctctgctttttgacagTCAATGTGCAATCATTATCTGGATCCCCTTCTAACTTCCAAGTTTACACTGCTTTATTGAAACCTCATGAGAGAATTATGGCACTTGATCTTCCCCATGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 5
ttgtacttaaatttatctagaatacttattctcaaaattttagttttctttctccaaaaaggtggcattctaact-------tgacaaccaattt--ctacctct-gcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
                                 ||| |  || |||  | | |   | ||    | | ||| | |       |||   |  ||||  ||   |||  |||||||||| |||||| | || || || ||||||||||||||||| ||||||||  | || || || ||||| |||||||||||  | ||||||||||||||
-------------------------------gtaaattactactttcatgtatatgagaaacaagaaatctgattagtcctttgatggcttatttgactggatcttacagTGAATGTTCAACCTTTGTCTGGATCTCCTGCCAACTTCCATGTGTACACTGCATTGTTAAAGCCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 5
ttgtacttaaatttatctagaatacttattctcaaaattttagttttctttctccaaaaaggtggcattctaacttgacaaccaatttc---tacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
     |      || |||    | ||| ||       |  |  |||||       || |  ||| ||   |   |  |     |||  |   |   | ||||||||| |||||  || |||| || || ||||| || || || ||||||||||| ||||| ||| | ||||| ||||| |||||  | ||||||||||||||
ccaggcgctgtgttttct---cttcttctttctcctttcctttttttcagcaggtaatagtgtgtcagctttgataaatgtttaatcacccttggttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAAGCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 5
ttgtacttaaat---ttatctagaatacttattctcaaaattttagttttctttctccaaaaaggtggcattctaa-cttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
 | |  ||||||   |||||||   |      || ||       ||   | |||||  | |        |||  || |||    |   |||| |   |  ||||| ||||||||  |  |||| || || ||||||||||| || | |||||| ||  |||| ||||| |||||||||||||||||  | ||||||||||||||
-tttgtttaaatcatttatctatt-tgtccgctcccacgtaaagagacatatttctgaacaccaactttatttaaagcttatttatttattttt--tttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 5
ttgtacttaaatttatctagaatacttattctcaaaattttagttttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctct---gcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
 |||  ||    || |      | |||  ||      |  |  |||||    |  || |  ||| ||   |   |  |     |||  |    | |   |||||||| |||||  || |||| || || ||||| || || || ||||||||||| ||||| ||||| ||||| ||||| |||||  | ||||||||||||||
ctgtgttttctcttcttcttctttctttctcctt---tcctttttttcagcatgtaatagtgtgtcagctttgataaatgtttaatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------ttgtacttaaatttat---ctagaatacttattctcaaaattt-----tagttttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
                                       |||  | ||||   |   ||  | | |   | ||    | |       ||| ||| |  |    | || || |  ||   ||  ||   |||  |||   |   ||||||| |||||  | || || || || || || ||||| || || ||||| || ||  |||| ||||||||| | |||||||| |||||||||||||||||
gtcagtcctctctgcttatgcatactcagttaccgaatctgttttcaaatacgtttgctgaagttcccttcctgcttactcggtagcagtattcgtcttttctagagatgcctatcatgctc-actttcaacgtctttttgaacagTGAACGTGCAGTCCCTGTCTGGATCGCCAGCAAACTTTCAGGTGTACACAGCTCTCCTGAAGCCACATGAGCGGATCATGGCGTTGGATCTTCCTCATGG

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:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|38472219|gb|CF956350.1|CF956350
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58691585|gb|CK080272.1|CK080272
EST:     CCAGAAACGTGC-TTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|29672938|gb|CB669213.1|CB669213
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|25798315|gb|CA754276.1|CA754276
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58661735|gb|CK050415.1|CK050415
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|84117692|gb|CD285458.1|CD285458
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|33800499|gb|CF326119.1|CF326119
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58689542|gb|CK078229.1|CK078229
EST:     CAGAAACGTGCTTTGGAGGCCTTCCGCTTGTGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CAGAAACGTGCTTTGGAGGCCTTCCGCTTG-GACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58609394|gb|CK037427.1|CK037427
EST:     CAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58691682|gb|CK080369.1|CK080369
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
                                        tttctacctct  CT-rich tract
                                      aatttcta  TA-rich tract