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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattttctctaacatctcaagtttcatgtactgataaatggcatttccagcccacttcttgatttgatgtgttctcattcagGATGAAGCTGGGACTGCAGCAATTAAGACAGTTGAACTTGACACCATGCTCGGAGGTCGTGCAGTGCAGCACAGAGAACTTCAAGGCTATGAATCTGATA

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 9
gtacattttctctaacatctcaagtttcatgtactgataaatggcatttc-ca-gcccacttctt-gatttgatg-tgttctcattcagGATGAAGCTGGGACTGCAGCAATTAAGACAGTTGAACTTGACACCATGCTCGGAGGTCGTGCAGTGCAGCACAGAGAACTTCAAGGCTATGAATCTGATA
                |  ||   ||   | | || |  | || |||||| || ||||||||||   |   | || || |  ||  |||||||||||||| || || || || ||||| |||||||| |||| |||||| |||||||| || ||||||||||| ||||  ||  |||| || || || |
--------------gtaggtcggattctctatgct-acgattgacatttcacacgcccacttctccaaaccgttgctgctaccacgcagGATGAAGCTGGAACCGCCGCGATCAAGACGGTTGAACTCGACAGCATGCTTGGAGGTCGCGCGGTGCAGCACAGGGAACCACAGTGCTACGAGTCCGACA

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 4
---gtacattttctcta---acatctcaagtttcatgtactg--ataaatggcatttccagcccacttcttgatttgatgtgttctcattcagGATGAAGCTGGGACTGCAGCAATTAAGACAGTTGAACTTGACACCATGCTCGGAGGTCGTGCAGTGCAGCACAGAGAACTTCAAGGCTATGAATCTGATA
   |||  |||||| |     |  ||||  | || |     |  | ||| | |||| |  |||||| | | ||       | || |||  |||||||||||||| ||||| || || ||||||||||| ||||||| ||||||||| || ||||| ||||||||||| || |  ||  |||| || |||||||
gtagtaggttttctgtgcctgctcctcagatctcctacgacgctacaaacgacattccgtgcccacctgtcgaaaactgttcttgtcacgcagGATGAAGCTGGAACTGCGGCGATCAAGACAGTTGAGCTTGACAGCATGCTCGGGGGCCGTGCGGTGCAGCACAGGGAGCCACAGTGCTACGAGTCTGATA

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 3
----------gtacattttctctaacatctcaagtttcatgtactgataaatggcatttccagcccacttcttgatttgatgtgttctcattcagGATGAAGCTGGGACTGCAGCAATTAAGACAGTTGAACTTGACACCATGCTCGGAGGTCGTGCAGTGCAGCACAGAGAACTTCAAGGCTATGAATCTGATA
           | | |||  ||| |  ||  || || ||  |   |  ||||  | |||       |  |    | ||   || || ||||  |||||||| |||| || ||||| || || || ||||| ||||| ||  | || ||||| |||||||| || |||||||||||||||||||| || ||||| |
gtattactacttccttttgttcttat-tcagaaattacacttgtagtaaaataacgtttatgcttgaaattgcaacttctggtcttatcat--agGATGAATCTGGAACAGCAGCTATAAAAACTGTTGAGCTTGATACTGTTCTTGGAGGGCGTGCAGTACAACACAGAGAACTTCAAGGCTACGAGTCTGACA

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S299_6V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------gtacattttctctaacatctcaagtttcatgtactgataaatggcatttccagccc--acttcttgatttgatgtgttctcattc---agGATGAAGCTGGGACTGCAGCAATTAAGACAGTTGAACTTGACACCATGCTCGGAGGTCGTGCAGTGCAGCACAGAGAACTTCAAGGCTATGAATCTGATA
                                                                             |   | ||    |    | |||  |  |    ||   ||     |   || ||| |    |  || ||       | |      |   ||||||||||||| ||||| |||||||| |||||||| || ||| |     | || ||||| || || ||  ||||||||  |||||   ||||| | ||| 
gtactctgatttcttggtcaagtgtgaatttgagcttccagtttttctgatatcttttgggtggttgaatagtcaaagccaacttcactttttctgtcatttacctcaaacctgtagtctactgctctagcgctagttggttaatgcatcacggttctgcccggcagGATGAAGCTGGCACTGCGGCAATTAAAACAGTTGAGCTGGACGCTGCTTTAGGTGGTCGCGCTGTTCAATACAGAGAAACTCAAGAACATGAAACGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactgataaatggcatttccagcccacttcttgatttgatgtgttctcattcagGATGAAGCTGGGACTGCAGCAATTAAGACAGTTGAACTTGACACCATGCTCGGAGGTCGTGCAGTGCAGCACAGAGAACTTCAAGGCTATGAATCTGATA
                                            ttctcattc  CT-rich tract
      ataaat  TA-rich tract