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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG

Basic information

species Oryza sativa
transcript LOC_Os03g16980.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
--------gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
        || |  || | |||     |||||    || | ||   ||||     | | ||    ||   |  ||  ||   ||||   | |||||||||  | |||||||||||| || || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||
ctaggtttgtggggctgagcaa----acattgaaatctagggtccttgct--atgggtcttgccttgcagacatgttggatgttgac--tttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 2
gtagaactcaacaat-gttgcattgttgcct-tgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
|| |   | | |||   ||| ||| | |  | | ||  |          | | ||    ||   |  |   ||   ||||   | |||||||||  |||||||||||||| || || ||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| ||||||||||
gtggggttgagcaaccattgaattctagggtctatgctatcatgctatgggtcttgtcttgcagacattttggatgttgac--tttgttcttttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 3
gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
       ||| |    ||   || |||  || |      | || |    |||||   |   |   | |     |     ||     |   ||||  |||||||||||| || || ||||  |||||||| ||||| |||||||| || || ||||| || || |||||||| ||||| || |||||||
------gtcagctg-attagtttattgtgtttttgagtagttttg----tttttcttttcaacgattctattatgcttacaaaacataacttctaatcagGTCATTGTTGCTGATAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTCGAGCTTATTCGTCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 3
gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
       | | | |  ||   || |||  || |      | || |    ||||    | || || |         | |  |    |   || ||  |||||||||||| || |||||||  |||||||| ||||| |||||||| || || ||||| || || |||||||||||||| ||||||||||
------gttagcta-attagtttattgtgtttttgagtagttttgt---ttttcttttcagcaattctattatgcttacaaaacataactt-ctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------gtagaactcaacaatgttgcattgttgccttgtgtgac-tgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
                                                                              | ||||    |   |   ||   ||     |  ||          |||  |     |||     |   |  ||   |  || | |   | | |  |||||| ||||| || |||||||  |||||||| || || |||||||| || || ||||| || || |||||||||||||| ||||||||||
gtaagtgggttatctatttgctcataatgttgtacttctgatgttcactcatgattttactgattttatacagatgccataacttgctatcatcctatatgtgataaataagatacagcatatagaactaagtttgacttgataaagttctgccacaatatctctgtgtttaatcagGTAATTGTTGCTGACAACTACTTCACTGGATCCAAGGACAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttt-tctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
                                                                            | | ||||    |   |   ||   ||     |  || | |     | |    ||  |  ||           ||    ||     ||||| | |  |||||||||||| || |||||||  |||||||| || || || ||||| || |||||||| || || |||||||||||||| ||||||||||
gtaagagggttatctatttgctcataatgttatatttctgatgttcactcatgattttactgactttatacagatggcataacttgctatcatcctatatgtgataaataaga-tacagcatatagaactaagtttgatttgataaaagttctgccacaaaatctttgtttaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 3
gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgtt--------cttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
||     |     || |    ||||| | | || |      ||   || | || | |    |   |       |   |  || |||         ||  |||  |||||||||||| || |||||||  |||||||| || ||||||||||| || |  ||||| || || ||||||||||||||||| |||||||
gttagcttggttgatatctttttgtt-cttagttttgaaatttattagttattcaacaagtacgatataactttggaacaatatgtgatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 3
gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgtt--------cttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
|| |   |     || |     |||| | | || |      ||   || | || | |    | | |       |   |  || |||         ||| |||  |||||||||||| || |||||||| |||||||| || ||||||||||| || || ||||| || || |||||||| |||||||| |||||||
gttggcttggttgatatctttctgtt-cttagtttttaaattttttagttattcaacaagtacaataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 2
--gtaga-actcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
  || || |     |  |  |   || ||   || | |   |  |   ||  |       | | | | ||      | ||     ||   ||| |||  |||||||||||| || |||||||| |||||||| || ||||||||||| || || ||||| || || |||||||| |||||||| |||||||
tggttgatatctttctgttcttagtttttaaattttttagttattcaacaagtac---aataaaacattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 2
gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
                             |||| |      ||| ||   ||||     ||   |  |     |||||   | |  | || |   |||||||  |||| || || |||| ||||||||| |||||||| ||||| |||||||||||||| ||||| || ||||| || || ||||| |
---------------------------gtttgtatacaaaattgacatgctttt---caagtttgatcatatttttgaaggtttcgttttattc-ttcagGTGGTTGTTGCTGATAACTATTTCACTGGCTCAAAAGAAAACCTCAAGAAGTGGATCGGTCACCCCAGGTTTGAACTTATTCGTCACG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagaactcaacaatgttgcattgttgc-cttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
                ||||||||     | | |  ||     | | || || |  ||      | |  |  |   || | || | || ||||     ||||| ||||| || || |||| ||||||||||||||| |||||||| ||||||||||| || || |||||||||||||| |||||||| |
--------------gtttgcattgaaattcctatccgatacaatagtagtttatgcgcgatttgattaagtactgatgtttatatttttttttac---cagGTGATTGTTGCTGATAACTATTTCACTGGTTCAAAGGACAACCTTAAGAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCACG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 3
gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgaga--aagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
|   |   || |||      | | ||| |   || | |||  || ||  ||   |  |        ||||     ||||| ||||  ||||||| || | |||| ||||| || || ||||  |||||||| || ||||| ||||||| ||| ||||| || || |||||||||||||| || |||||||
gattataccaccaaaaagaaaattttgaccaatgcgtctgtctgtcatgttacaatgtatccttgggtgcttatatttga-catgctttctttt-tgcttagGTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG

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|29668686|gb|CB664961.1|CB664961
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58659240|gb|CK047920.1|CK047920
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|313080404|gb|HO213412.1|HO213412
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAATCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|33675428|gb|CF303667.1|CF303667
EST:     GTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: GTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|428184|gb|D24332.1|D24332
EST:     GACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAG-NAACNTTTTTCACTGGTTCAAAAGACAACCTGAAGAA
genomic: GACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAAC-TTTTTCACTGGTTCAAAAGACAACCTGAAGAA
EST: gi|30229035|gb|CB966926.1|CB966926
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|30228342|gb|CB966233.1|CB966233
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|29668646|gb|CB664921.1|CB664921
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58672962|gb|CK061648.1|CK061648
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58654932|gb|CK043612.1|CK043612
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCGTGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|33380802|gb|CF196145.1|CF196145
EST:     AACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: AACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58656016|gb|CK044696.1|CK044696
EST:     TCATCGGCGCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58659773|gb|CK048453.1|CK048453
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|30226636|gb|CB964528.1|CB964528
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG
                           ctttgat  putative branch site (score: 5)
                                      tgttcttttctgttc  putative PPT
                                        ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - -atgttgc
- - - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - - - - - -ctgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - ttagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcgggc