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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatccgtagcaaagcaagtgtatttagctagtatagaataaaatgtatacaaattttggtttagaactcctgacaattaacccttctttgtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTTCAGCTTCAGGTCAAG

Basic information

species Oryza sativa
transcript LOC_Os06g09370.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09370.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G024530_T01 (Zea mays), 3'ss of exon 6
---taatccgtagcaaagcaagtgtatttagctagtatagaataaaatgtatacaaattttggtttagaactcctgacaattaacccttctttgtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTTCAGCTTCAGGTCAAG
   |     | |  | ||||  | ||  |  ||   |     |  | | | |  || | |    ||  |     ||    ||      |  |  |   |||||||||| |||||||| ||||| |||||||| |||||| |||||||||||||||||||||||||||||
ccatgccaaggaatacagcagttttacctttctttaaagacgtttattttgtttaattctc---ttgaataagatggagtttcgaatcttatgatgcaagcagGCAGACAAGGCATCCATGCTGGATGAAATCATTGATCATGTGAAATTTCTTCAGCTTCAGGTCAAG

upper sequence: LOC_Os06g09370.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G116785_T01 (Zea mays), 3'ss of exon 4
taatccgtagcaaagca---agtgtatttagctagtatagaataaaat-gtatacaaattttggtttagaactcctgacaattaacccttctttgtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTTCAGCTTCAGGTCAAG
    || |||||| | |   |      ||| ||   ||  || |   |  | |    | ||   || | ||            || | ||  | ||   |||||||||| |||||||| ||||| |||||||| |||||||||||||| |||||||||||||||||||||
--taccatagcaaggaagacaacagtcttacctttcattaaagaggttcatttgtttagttctcttaataatatggagtggcaaatcttt--tggtgcaagcagGCAGACAAGGCATCCATGCTGGATGAAATTATTGATTATGTGAAGTTTCTTCAGCTTCAGGTCAAG

upper sequence: LOC_Os06g09370.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv11s0016g00380.t01 (Vitis vinifera), 3'ss of exon 4
taatccgtagcaaagcaagtgtatttagctagtatagaataaaatgtatacaaattttggtttagaactcctgaca----attaacccttctttg-tatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTTCAGCTTCAGGTCAAG
  |||   ||  | | |  ||| ||     ||  || | |  |  | | || | |    |   || ||||   | |    | | |  | | |||| | |  |||| | || || ||||| ||||| || ||||| ||||| || || |||||||||||||| |||||||||
--atctcaagttaggaacatgtgttcgaggagctta-attgtatggaagaccattcacag--caggactctaaaaagagtactgattcctttttgctttctgcagACGGACAAAGCATCTATGCTCGACGAAATCATTGAGTACGTCAAATTTCTTCAGCTCCAGGTCAAG

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|87012724|gb|CI295168.1|CI295168
EST:     TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG                         GCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
genomic: TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAGgtgctttttt ... gtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
EST: gi|88980643|gb|CI026705.1|CI026705
EST:     TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG                         GCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
genomic: TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAGgtgctttttt ... gtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
EST: gi|218483231|gb|FG956163.1|FG956163
EST:     TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG                         GCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATT-CTT
genomic: TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAGgtgctttttt ... gtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
EST: gi|86498321|gb|CI140954.1|CI140954
EST:     TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG                         GCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
genomic: TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAGgtgctttttt ... gtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
EST: gi|5039098|gb|AU071208.1|AU071208
EST:     TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG                         GCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
genomic: TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAGgtgctttttt ... gtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
EST: gi|218482847|gb|FG953463.1|FG953463
EST:     TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG                         GCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT
genomic: TTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAGgtgctttttt ... gtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatacaaattttggtttagaactcctgacaattaacccttctttgtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTTCAGCTTCAGGTCAAG
                              aattaac  putative branch site (score: 2)
                                    cccttctttgt  CT-rich tract
      aaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatccgtagcaaagcaagtgtatttagctagtatagaataaaatgtatacaaattttggtttagaactcctgacaattaacccttctttgtatgagcagGCAGATAAGGCATCAATGCTTGATGAAATAATTGATTATGTGAAATTTCTTCAGCTTCAGGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT