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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattgtcatcgaacaaagcaactgatatattgcgcattattgtttcatgtttgtactttatttcataatattttctaatgcattattgtccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g13730.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13730.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 15
------ttattgtcatcgaacaaagcaactgatatattgcgcattattgtttcatgtttgtactttatttcataatattttctaatgcattattgtccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG
      | ||| |||||      |   ||   |||     |  ||   |    | ||||     ||   |  |  ||| |      |||    |||   | |||||||||||||| | || |||| ||| ||||| ||||  |||||| | ||||||||||| ||||| || || ||||||||||||||||| ||
aggcaataattttcatcagttgtacttaccactattggaagagtttaaga---acgttttgctgttgacttgttgtatgtgactgagcaaatatgt---tgtgcagCTTCTTCCACGGGAGCGCAAAAAGCAAGAGTACCAGGATGCTTTGAAGGAGCGGTACAAGCATCTCCCAGAAGTCAAGCGGATTGTAAG
















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|218501280|gb|FG957978.1|FG957978
EST:     TCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: TCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|218494779|gb|FG960743.1|FG960743
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|86260043|gb|CI065916.1|CI065916
EST:     TCAGAACAGTTGGGAGTC                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: TCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|88347170|gb|CI631250.1|CI631250
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|88305455|gb|CI630617.1|CI630617
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTACATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|58676735|gb|CK065422.1|CK065422
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGT
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGT
EST: gi|89192699|gb|CI049997.1|CI049997
EST:     TCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: TCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|88385229|gb|CI630330.1|CI630330
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|87035464|gb|CI190086.1|CI190086
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|87040354|gb|CI194976.1|CI194976
EST:     TCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: TCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|218502449|gb|FG965484.1|FG965484
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|3759655|gb|C96913.1|C96913
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|88348688|gb|CI631382.1|CI631382
EST:     ATACGAATCTTCGGCTGTGGAAGTCCACAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG
EST: gi|88351589|gb|CI628809.1|CI628809
EST:     ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTT                         CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTACATGCTGTCAAGGAG
genomic: ATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAG

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: 70 (upstream exon), 73 (downstream exon)
Score: 41

TTGTGTGAAATACACCTATGATGGAACCTATTTGGTTTCTGGCAGTGATGATACGAATCTTCGGCTGTGGAAGTCCAAAGCTTCAGAACAGTTGGGAGTTgtaagtttct ... ccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtttgtactttatttcataatattttctaatgcattattgtccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG
                            ttctaat  putative branch site (score: 41)
                                         ttgtcctttt  putative PPT
         tactttatttcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattgtcatcgaacaaagcaactgatatattgcgcattattgtttcatgtttgtactttatttcataatattttctaatgcattattgtccttttgcagCTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - -gaacaaa
- - - - - - - - - gcaactg
- - - - - - - - - - - - - - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatt