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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgaaaggcctccttcatctgcattctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcatattttccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC

Basic information

species Oryza sativa
transcript LOC_Os03g28410.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G04890.1 (Glycine max), 3'ss of exon 1
---------------------------atgtgaaaggcctccttcatctgcattctca------taag---cgatagattcttgatta----tgtaacaatggtgatgacaagaggctatccttg------catattttcct-------------tcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
                            | | |  |  |||   ||   ||||  | |      |||    | || |||  ||| ||     || || | | || ||     ||    ||  |||        | || | ||             | ||| |||| ||| ||||||||||| || || ||||||||||||||||| || || || || || ||||| ||||||||||| ||||| ||||| || || ||
gtaactaaaaccctagctcatcctctcttttcatcgatctctgacaatcgcatgttaaacaatttaaattccaatggatgtttgtttgaacctgcaatagttgtaatagacggatttgatttttgatttgctgtgttgtgctgtggattttggaattagGGATTTACATTATTAACCTTGGGAAGACGTGGGAGAAGCTTCAGCTAGCAGCTAGGGTTATAGTTGCAATTGAGAACCCCCAGGATATCATTGTTCAATC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G17000.1 (Glycine max), 3'ss of exon 1
atgtgaaaggcctccttcatctgcattctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcatattt------------tccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
            |  ||  | || |      | |  ||    ||| |  |  |     ||| | ||      |  | | |  ||| || |||            |  |||||| |||| ||| ||||||||||| || || ||||||||||||||||| ||||| ||  | || || |||||||||||||||||||| |||||||| |||||
-----------tttttttttttgtaccgctgtta-tgaagatttcctcttgctactgaaatagagacattttggagtttttgttgaatttttgtggtttatgtttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTGCTAGGATTATAGTCGCCATTGAGAACCCACAGGATATCATCGTTCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G42150.1 (Glycine max), 3'ss of exon 1
atgtgaaaggcctccttcatctgcattctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcatattttc---------cttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
         |  | |||  | ||||     |  |  ||  | ||| |  |  |     ||| |  |      |  | | |  ||| || |||            |||||| |||| ||| |||||||||||||| || ||||||||||| ||||| ||||| ||  | |||||||||||||||||||||||||| ||||| || |||||
------ggcgtttgcttt-tttgcaccgctacca-tgaaggtttcctcttgctactgaaatag-aacattttggagtttttgttgaatttttgtggtttatgttttcagGTATTTACATAATTAACCTTGGCAAGACATGGGAGAAGCTCCAGCTCGCTGCTAGGATTATTGTTGCCATTGAGAACCCACAGGATATCATTGTTCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G01460.1 (Glycine max), 3'ss of exon 1
-----------atgtgaaaggcctccttcatctgcattctcataag---------cgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcatattttcct------------------tcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
            |         ||| || |||  |    | | ||          | || |||  |||| | || || |   || ||      |    ||  |    |  |||  |                  | ||| |||| ||| ||||||||||| || || ||||||||||||||| | || || || || |||||||| ||||||||||| ||||| ||||| || || ||
gtaactgaacttttctcgttctctcttttatcatctcgttaaaaaaattaaatttcaatggatgtttgaatctgcaatagctgtaatagaggaattgaattttgatttgatttggtgtggtttggatttgggaattagGGATTTACATTATTAACCTTGGGAAGACATGGGAGAAGCTTCAGTTAGCAGCTAGGGTTATTGTTGCAATTGAGAACCCTCAGGATATCATTGTTCAATC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G72370.2 (Arabidopsis thaliana), 3'ss of exon 1
atgtgaaaggcctccttcatctgcattctcataagcgatagattcttgattatg--taacaatggtgatgacaagaggctatccttgcatatttt----ccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
                |  | ||  || |  |      |  ||| |   |||    |   | ||||||  |    |     |  ||| |  |||        ||||| |||| |||| | |||||||||||||| ||||| ||||| ||| ||||||| ||||| ||||||||||||||||||||||||||||||||||| |||||
------gtatttgtgctagtgtgtgttattgttgctcttttattgtaatttacaattgtaagtggtgagtatggaacttagtttttgaagttttcgtcattctcagGTATTTACATCTTCAACCTTGGCAAAACATGGGAAAAGCTCCAGATGGCTGCTAGAGTTATTGTTGCCATTGAGAACCCACAGGACATCATCGTCCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 3'ss of exon 1
atgtgaaaggcctccttcatctgcat--tctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcatattttcct-----tcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
     |    |  |    |    |||  | | ||    ||| | || |||   || | | |||| |  || ||| |   ||   |    | | || ||     ||||| |||| |||||| |||||||| ||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||||||  |||||||||| || |||||
-----accatctgcggaaaataacatgatttgatggatgatcggtt-ttgtagatatga-aatgattttgccaaaattttaagatcttttgtctttctaatgatcagGGATTTACATCATCAACCTTGGAAAAACATGGGAGAAGCTGCAGCTTGCAGCCAGGGTGATTGTTGCGATTGAGAACCCTAAGGACATCATTGTTCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S173_16V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------atgtgaaaggcctcc--------ttcatctgcattctcataagcg---atagattcttgattatgtaacaatggtgatgacaagaggctat--ccttgcatattt-tccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
                                                                                     |||  || ||             | ||  |   || |   | | |   |||  || | ||           | | | ||         | |  | | ||   |   |    |||| ||||||||||||||  | || || || |  ||||||||  ||||||| || || ||||||| |||||| |||||||| ||||||||||| ||||||||
gtgagaactctgtcccctccattgtttgtcctcgtcccggtgtgttatcggtgtgggcttggggtgagaagtttctgtgttatgaatgataagggttcggggtgaagatacaagtttttttttggacgtgtgtatatgttttggacgggtcgtggtttggggtggttgactattgtggcttggcgggtccgttgcgcagGTATTTTCATCATTAATGTGGGAAAGACTTACGAGAAGCTGGAGCTGGCGGCGAGGGTGATTGCTGCCATCGAGAACCCTCAGGACATCATTGTGCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S209_48V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------atgtgaaaggcctccttcatctgcattct-cataagcgatagattcttgattatgtaacaatggtgatgacaa-gaggctatccttgcatattttcctt-cagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
                                                                         |||   || |  |       |  |  | |  | |  || | ||  |||   ||    | ||  || |  |  | ||   |  ||  ||  | |     |||||||||||||||| ||| | ||||| ||||  ||||||||  ||||||| || || ||||||| |||||| |||||||| |||||||||||||| |||||
gtaattagggctttttccccctgtggcccgtgttggggtttggttgggtgcgtgtgcgagtgttcgttttttggtgcgggggcggcgcggggggtttggtgcggatggaattggtttgtgaaggtgggcgattgacgagggtagtggggtcgttgttttattctgtgtgggcagGCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------------------atgtgaaaggcctccttcatc-tgcattctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcatattttccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
                                                                                                    || | || || | |  | |  | | |     |  | |   |        |   |||    ||||| | ||||   | |       |  ||       |||||||||| || || ||| ||||||| ||||  ||||||||| |||| ||||| || |||||||  ||||| |||||||| |||||||| |||||||||||
gtattaattctcattagggttattccttagacaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgcagcgttgttcgtaacgttgcgtgccggtgctgccctccggtatgtgtggtggtaacaatgtggt-------cgcatcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------atgtgaaaggcctccttcatc-tgcattctcataagcgatagattct--------tgattatgtaacaatgg--tgatgacaagag----gctatccttgcatattttcctt---cagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
                                                 |||| |||   || ||  |  |||     |    | | | | |||         || || ||| | | |||  || |||| || |    |   || ||   ||||||   |   |||| ||||||||||| ||  | ||||| ||||  || |||||  ||||||| || || ||||||| |||||| |||||||| |||||||||||||| |||||
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtt-tgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ32709 (Selaginella moellendorffii), 3'ss of exon 1
atgtgaaaggcctccttcatctgcattctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcat-attttccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
                                                     ||||  ||  |  |  |     || ||| | || |  |  | |  ||||||| |||||||| ||  | || || || ||||||||||| ||||| || ||| | |||||||| | ||| |||||||| || || ||||||||||||||
-----------------------------------------------------gtaa-gatcctagtcgcttctcgcgatcttagctttgtggtgccacagGCATCTTCATCATCAATGTCGGGAAGACGTGGGAGAAGCTCCAGCTCGCGGCCCGCGTGATTGTGGGCATCGAGAACCCCCACGATATCATCGTGCAGTC

upper sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ20712 (Selaginella moellendorffii), 3'ss of exon 1
atgtgaaaggcctccttcatctgcattctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcat-attttccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
                                                     ||||  ||  |  |  |     || ||| | || |  |  | |  ||||||| |||||||| ||| |||| || || ||||||||||| ||||| || ||| | |||||||| | ||| |||||||| || || ||||||||||||||
-----------------------------------------------------gtaa-gatcctagtcgcttctcgcgatcttagctttgtggtgccacagGCATCTTCATCATCAACGTTGGGAAGACGTGGGAGAAGCTCCAGCTCGCGGCCCGCGTGATTGTGGGCATCGAGAACCCCCACGATATCATCGTGCAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattatgtaacaatggtgatgacaagaggctatccttgcatattttccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC
      atgtaac  putative branch site (score: 3)
                                          tattttccttc  putative PPT
                                         atatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgaaaggcctccttcatctgcattctcataagcgatagattcttgattatgtaacaatggtgatgacaagaggctatccttgcatattttccttcagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC

- - - - - - - cttcatc
- - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - -attcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg