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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgtttcatccttccgaaccatttatgttttgtgtgatagcatctgtattcatctacatgtcacggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG

Basic information

species Oryza sativa
transcript LOC_Os05g41110.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 3
gtaagtttgt-ttcatccttccgaaccatttatgttttgtgtgatagcatctgtattcatctacatgtcacggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG
|||||      |||| |||| |       |||| | |||   ||| |  | |  ||| |  ||  ||  |   |      || |||||  ||   |||   | | | |||          |||||||||||||||||||||| ||||||||||||||||||||| |||||||||||||||| ||||||||||| |
gtaaggccaccttcaccctttcagg---attatctattgcaagat-gtgttttgatttagttatttgctagtat------gtaatata--ttaacact---tttttgact----------tttcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 3
-------------gtaagtttgtttcatccttccgaaccatttatgttttgtgtgatagcatctgtattcatctacatgtcac--ggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG
              | | | || || || | |    |  |      ||   || |       |  |   ||| ||  |||      |     || |       |    | ||     ||   | |||||||| | | ||||||| ||||| || || ||||||||||||||||||||||| ||  ||   ||   ||||| |||||| |
gtaagtggcggtcctcaatatgcttgatgcctagtcaataccggc-ttccatggggctttggcgctgcgcatttatttgttgttgagcgcacccattgcccgctgctttcctcaccttccctccgtgccttc-cctccagACAACGTTGACCTGGGCACTGCCTGCGGCAAGTACTACCGCGTCAGCGTGCTGGCCATCACCGACCCCG
















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|88208991|gb|CI208840.1|CI208840
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|30228744|gb|CB966634.1|CB966634
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|88281712|gb|CI403108.1|CI403108
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|14981077|gb|BI305768.1|BI305768
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|25797182|gb|CA753143.1|CA753143
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|27578251|gb|CB000946.1|CB000946
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|30228625|gb|CB966515.1|CB966515
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|87025758|gb|CI282335.1|CI282335
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|87023003|gb|CI280020.1|CI280020
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|58594776|gb|CF993084.1|CF993084
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|87032220|gb|CI262002.1|CI262002
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86593179|gb|CI255641.1|CI255641
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|53553193|gb|CO435745.1|CO435745
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|88995949|gb|CI037240.1|CI037240
EST:     TTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|29686201|gb|CB682476.1|CB682476
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86530215|gb|CI170421.1|CI170421
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|58031073|gb|CX728616.1|CX728616
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|87011660|gb|CI281362.1|CI281362
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86532355|gb|CI172561.1|CI172561
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|88241578|gb|CI241427.1|CI241427
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86417527|gb|CI031736.1|CI031736
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|88547996|gb|CI478330.1|CI478330
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|88400326|gb|CI591016.1|CI591016
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86599456|gb|CI251414.1|CI251414
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|88556598|gb|CI486936.1|CI486936
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86533322|gb|CI173528.1|CI173528
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|55410942|gb|CV723318.1|CV723318
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86416886|gb|CI030897.1|CI030897
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86835219|gb|CI346694.1|CI346694
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|86529357|gb|CI169563.1|CI169563
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
EST: gi|88991955|gb|CI035093.1|CI035093
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 69 (downstream exon)
Score: 113

AAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGATTGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG
                               gtcttac  putative branch site (score: 113)
                                          ccttcgctttc  putative PPT
            atatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgtttcatccttccgaaccatttatgttttgtgtgatagcatctgtattcatctacatgtcacggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC