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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaattgccatgccatagtcttatttttttagatcaatctgttcatcttgcttgcttactttgttttcggagaagttattaatgtgtatactgatgggaccaatatcttgctttctaattttctttttaagCAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAG

Basic information

species Oryza sativa
transcript LOC_Os08g14460.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 6
gtagaattgccatgccatagtcttatttttttag-atcaatctgttcatcttgcttgcttactttgttttcggagaagttattaatgtgtatactgatgggaccaatatcttgctttctaattttctttttaagCAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAG
      ||    |||| || | |  |  ||  || ||||  ||   |||   || || ||| |||||| | | |    |  ||  ||   |      | | |||  |      |||  |   ||  | |  ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| || ||||||
-----gttagactgccttattttattccttcgagtatcatcctaaccata--gcatgtttattttgttattgcattgatatttggtgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG

upper sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 6
gtagaattgccatgccatagtcttatttttttagatcaatctgttcatcttgcttgcttactttgttttcggagaagttattaatgtgtatactgatgggaccaatatcttgctttctaattttctttttaagCAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAG
                             ||  ||    | |||| |  ||   |  ||| |   | ||  | |||  |       |  || || |  | |   | ||| |  ||  | ||  |      ||||||||  | || || ||||||||||| ||||||||||||||||| |||||||| |||||||||
----------------------------gttaggactcttttgttaa--ttatctagttagtgcttgttatgtgaaaatgc----atagattctaaaagcattca-atcctatttgtttatggtgcca--aagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaatgtgtatactgatgggaccaatatcttgctttctaattttctttttaagCAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAG
                                    ttctaat  putative branch site (score: 2)
                             tcttgctttctaattt  CT-rich tract
                                   tttctaattttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaattgccatgccatagtcttatttttttagatcaatctgttcatcttgcttgcttactttgttttcggagaagttattaatgtgtatactgatgggaccaatatcttgctttctaattttctttttaagCAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA