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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCAAATTACTCCGGAAAGAAGGGCAAAAGATCAAAGAGGAAGCGCATGGTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtactatgaacacacaaacacctttttataaagaagctcactagcttatttgaattctggagttcatgttttttaagtggcaaaaaagaaaggtttatactctatcttatcatatgtccttgatcaattggtgttaatgtcatgtacatttacaaatacag

Basic information

species Oryza sativa
transcript LOC_Os01g05800.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G110063_T01 (Zea mays), 5'ss of exon 12
--TTCCAAATTACTCCGGAAAGAAGGGCAAAAGATCAAAGAGGAAGCGCATGGTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtactatgaacacacaaacacctttttataaagaagctcactagcttatttgaattctggagttcatgttttttaagtggcaaaaaagaaaggtttatactctatcttatcatatgt--ccttgatcaattggtgttaa-tgtcatgtacatttacaaatacag-------------------------
   ||||| |||||| || ||||||||||||||||| ||||||||||||||||| ||||    || ||||  |   || ||||   ||||| | ||  |||||||||| ||||  || | || | || | || |  | ||| | | | |        ||   || | ||| || || |     |  ||||||| |||    || ||  |  |||    |  ||  |||   | ||||   |||   ||  | |   |    |||    |                          
GCCTCCAAGTTACTCAGGGAAGAAGGGCAAAAGATCCAAGAGGAAGCGCATGGTGCAGTGATCGTCACAG--CTCAATCGGATGCGATTTTCGCCACAACTGgtaagtgctattgaccctcagatac-tgttcacgacgaatcacgccacggacacagagaactagggttgatcttctcccttttacaaaaaaaaaaatgatagacggttccttgctgttcgtttcctcagtaaattaaggttttctgaaacgggtaccctcaacagaaaacatgacaatagtttgccattgcag

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G839422_T01 (Zea mays), 5'ss of exon 11
--TTCCAAATTACTCCGGAAAGAAGGGCAAAAGATCAAAGAGGAAGCGCATGGTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtactatgaacacacaaacacctttttataaagaagctcactagcttatttgaattctggagttcatgttttttaagtggcaaaaaagaaaggtttatactctatcttatcatatgtccttgatcaattggtgttaatgtcatgtacatttacaaatacag
  ||||||| ||||| || ||||||||||||||||| ||||||||||||||||| |||||   ||  ||| |  | |||||||   ||||||||||  |||||||||| ||||  || | || | || | || |||| ||| |     |             |  | ||| |  || |     | | ||||||      ||  |||| |  |||                                                     
ACTTCCAAACTACTCAGGGAAGAAGGGCAAAAGATCGAAGAGGAAGCGCATGGTGCAGTAATCGTTGCAGCA--TAATTGGATGCGATTTTTGTCACAACTGgtaagttctattgaccctcagatac-tgttcataatgaatcatgtca------caaggaaccagggttgaacttctccgttttgtaaaaaa------ttcttactgttccttt----------------------------------------------------
















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|89173571|gb|CI041464.1|CI041464
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88983200|gb|CI020764.1|CI020764
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88533579|gb|CI461154.1|CI461154
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCANTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88502172|gb|CI429678.1|CI429678
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTANTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88525355|gb|CI454345.1|CI454345
EST:     GTTCANTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|86905375|gb|CI285338.1|CI285338
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|86853625|gb|CI330476.1|CI330476
EST:     TTCAGTAGGGTTTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAATTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: TTCAGTA-GGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|29615537|gb|CB620549.1|CB620549
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|13896050|gb|AU182386.1|AU182386
EST:     TGACAAAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACCCAATTTT
genomic: TGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|33381936|gb|CF197279.1|CF197279
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|4714906|gb|AU056023.1|AU056023
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88514031|gb|CI441537.1|CI441537
EST:     TTCAGTAGGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: TTCAGTA-GGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|66916771|gb|CX103619.1|CX103619
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|4716265|gb|AU057381.1|AU057381
EST:     ACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCNGTACGGTTGTGTAGTTGATCTCGGACCCAATTTT
genomic: ACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88536938|gb|CI464742.1|CI464742
EST:     TTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGGTGATCTCGGACACAATTTT
genomic: TTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|89175661|gb|CI042682.1|CI042682
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88837819|gb|CI079179.1|CI079179
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88509790|gb|CI437296.1|CI437296
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88530676|gb|CI459090.1|CI459090
EST:     TTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: TTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88994803|gb|CI036384.1|CI036384
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88516853|gb|CI442509.1|CI442509
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|14713818|gb|AU197781.1|AU197781
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGG
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGG
EST: gi|88284718|gb|CI406164.1|CI406164
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|86863949|gb|CI332899.1|CI332899
EST:     TTGGATTTCATTTTTATCATTACTG                         GTTAATTCAATT-GCCAGTACGGGTTGTGTAGTTGATCTCGGACACAATTT
genomic: TTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTAC-GGTTGTGTAGTTGATCTCGGACACAATTT
EST: gi|88536527|gb|CI466286.1|CI466286
EST:     TGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTT
genomic: TGACAGAACCTGATTGGATTTCATTTTTGTCATTACT-Ggtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTT
EST: gi|88545703|gb|CI475282.1|CI475282
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|4714905|gb|AU056022.1|AU056022
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88478934|gb|CI416205.1|CI416205
EST:     CATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: CATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|88510769|gb|CI438275.1|CI438275
EST:     CCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: CCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|29620328|gb|CB625340.1|CB625340
EST:     GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: GTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|89182402|gb|CI113771.1|CI113771
EST:     TGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: TGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
EST: gi|86524025|gb|CI164231.1|CI164231
EST:     TGTGACAGAACCTGATTGGATTTCATTTTGGTCAGTACTG                         GTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT
genomic: TGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTT

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), 75 (downstream exon)
Score: 51

TTCCAAATTACTCCGGAAAGAAGGGCAAAAGATCAAAGAGGAAGCGCATGGTTCAGTAGGTGTGACAGAACCTGATTGGATTTCATTTTTGTCATTACTGgtaagtacta ... acaaatacagGTTAATTCAGTTGGCCAGTACGGTTGTGTAGTTGATCTCGGACACAATTTTGATGATCAGTTGGGAAGGCTAATCTTCAGGTGCAGGACAGACACGAAAC




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