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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccatccgttcgttcttgattcttcatcctcgttgccgccattgatcaggattcagaagttctttgtgataaccaaattcactggcttcaatgaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTGCCCTACTTCTACTCCCGGTCGTTCGACCTCTCGTGGCAGTTCTACGGCG

Basic information

species Oryza sativa
transcript LOC_Os08g44340.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S90_28V6.4 (Physcomitrella patens), 3'ss of exon 10
gtgagccatcc-gttcgttcttgattcttcatcctcgttgccgccattgatcag-gattcagaagttctttgtgataaccaa-----attcactggctt------caatgaacttg-cagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTGCCCTACTTCTACTCCCGGTCGTTCGACCTCTCGTGGCAGTTCTACGGCG
||  |  |||| ||| | |  |  |||  |   ||  |    |     | |||| | ||    | |||| | |||  |  |      ||    | ||||      |||  |  | | ||||||||||| ||    |||   |||||    |||   |||||||| ||||| || | |||||||||||| || ||| | || |||||||||||||||||||
gtatgttatcccgtttgcttgtacttcgacgatcttttgaatgaagaggttcagtggtttgtgacttctctatgaggataattttttatctgatagcttgtgaatcaacaatttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTCCCATTCTTCTACTCCCGCTCCTTCAATCTGTCGTGGCAGTTCTACGGCG

upper sequence: LOC_Os08g44340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S237_59V6.1 (Physcomitrella patens), 3'ss of exon 10
---------gtgagccatccgttcgttc--ttgattcttcatcctcgttgccgccattgatcaggattcagaagttctttgtga-taac-----caaattcactggcttcaatgaacttg----cagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTGCCCTACTTCTACTCCCGGTCGTTCGACCTCTCGTGGCAGTTCTACGGCG
          | | |||    ||||| |  | | |  |  | ||    |       |   | |    | | |  ||| |||| | | ||      | ||| |   | |  |||      |    ||||| ||||| ||    |||   |||||  | |||   || |||||||||||||||| ||| ||||| || || ||||||||||| ||||| ||||| || |
gtttgtaatataacccaagttttcgtccaatcggtattctaccccgtgtattctggtaatttaactcttacattttcgttgtaaatcacgcctttatattgaaatgttcaaattgttgcgaatccagGCCATCAAAGCCGCTGAGAAAGGCGAAACTGTGGACGACTACGACTACCTGCCCTTCTTTTACTCACGATCTTTCGACCTCTCATGGCAATTCTATGGAG
















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|29662249|gb|CB658524.1|CB658524
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|218482645|gb|FG946342.1|FG946342
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|33793845|gb|CF322810.1|CF322810
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86495616|gb|CI138249.1|CI138249
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|88215349|gb|CI215198.1|CI215198
EST:     GCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|33681536|gb|CF309775.1|CF309775
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGGGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86494248|gb|CI136881.1|CI136881
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|33691642|gb|CF319881.1|CF319881
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGAAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86502838|gb|CI145471.1|CI145471
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|88210081|gb|CI209930.1|CI209930
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86824305|gb|CI262876.1|CI262876
EST:     GCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|89186511|gb|CI048183.1|CI048183
EST:     TGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: TGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|33794498|gb|CF323136.1|CF323136
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|88205279|gb|CI204665.1|CI204665
EST:     TCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: TCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|33681535|gb|CF309774.1|CF309774
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGGGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|38480742|gb|CF964831.1|CF964831
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86434849|gb|CI106082.1|CI106082
EST:     AGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: AGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86828658|gb|CI278729.1|CI278729
EST:     CAGCCGAGCAGGCCGTGAAG                         GCGATCAAGTCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: CAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86493369|gb|CI136002.1|CI136002
EST:     GCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86488925|gb|CI131558.1|CI131558
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|87035169|gb|CI189791.1|CI189791
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|86500421|gb|CI143054.1|CI143054
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|218492958|gb|FG966645.1|FG966645
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|88218699|gb|CI218548.1|CI218548
EST:     TAGAGCATGTGGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: TAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|29636699|gb|CB641708.1|CB641708
EST:     GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCTGAGCAGGCTGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: GAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
EST: gi|88993366|gb|CI257794.1|CI257794
EST:     AGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAG                         GCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG
genomic: AGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTG

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: 73 (upstream exon), 73 (downstream exon)
Score: 26

CATTGCCGACGTGGCCGCCTTCCCGATGAAGCTATACAATGAGATTAGGAGAGTAGAGCATGTTGACCATGCTCGCAAATCAGCCGAGCAGGCCGTGAAGgtgagccatc ... gaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTGCCCTACTTCTACTCCCGGTCGTTCGACCTCTCGTGGCAGTTCTACGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggattcagaagttctttgtgataaccaaattcactggcttcaatgaacttgcagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTGCCCTACTTCTACTCCCGGTCGTTCGACCTCTCGTGGCAGTTCTACGGCG
                   tgataac  putative branch site (score: 26)
                           aaattca  TA-rich tract