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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcattgtttctcttgaaacttctttctgtgctgcttctagctagtgtcgtatatatagtttcagatgcctgatcgttaacctatggttgttggtgttttctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAGAATGTGGCGAGTAGGGTTGGACACAAATTCCTTGAGGATGGAACGAAGG

Basic information

species Oryza sativa
transcript LOC_Os06g46930.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G36150.1 (Glycine max), 3'ss of exon 3
gtcagcattgtttctcttgaaacttctttctgtgctgcttctagctagtgtcgt-atatatagtttcagatgcctgatcgttaac-ctatggttgttggtgttttctttga---tcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAGAATGTGGCGAGTAGGGTTGGACACAAATTCCTTGAGGATGGAACGAAGG
              |||      ||| || | |  |   | ||   ||  |  |  |  || | |  | ||     |    |||  || | |       |||||| ||| |    ||||||||||| || || |||||||||||||||||||||||||| || ||  |||| || || ||  | || || || ||| |||||||  |||| |  || |
--------------tctca----ttcattgtttattatgtataagcagaataattgtccattggtgtatattttcaacgactaatacttttgagaaacatgttttttttaaattccagATTGAAGGTCCTATCCACAGCTCAAATGTGATGCTCTACTCCAAAGATCAGAAGGTAGCAAGCCGTGTGGGGCATAAAGTCCTTGATAATGGTAAAAAAG

upper sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G34400.1 (Glycine max), 3'ss of exon 3
gtcagcattgtttctcttgaaacttctttctgtgctg--cttctagctagtgtcgt-atatatagtttcagatgcctgatcgttaacctatggttgttggtgttttctttgat--cagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAGAATGTGGCGAGTAGGGTTGGACACAAATTCCTTGAGGATGGAACGAAGG
                 | | | ||  |  |          | ||   ||  | ||  |  || | |  | |||    |    |||   ||  | |      |||| ||| ||  ||||||||||| || || |||||||||||||||||||||||||| || ||  |||| || || ||| | || || || ||| |||| ||  |||| |  || |
-----------------taatatttactgataaagaaaatgtataagcagaatagttgttcatgggtgtatatgttcaacaactaata-attttgggaaacattttttttaattccagATTGAAGGTCCTATCCACAGCTCAAATGTGATGCTCTACTCCAAAGATCAGAAGGTAGCAAGTCGTGTGGGGCATAAAGTCCTAGATAATGGTAAAAAAG

upper sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G34400.2 (Glycine max), 3'ss of exon 3
gtcagcattgtttctcttgaaacttctttctgtgctg--cttctagctagtgtcgt-atatatagtttcagatgcctgatcgttaacctatggttgttggtgttttctttgat--cagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAGAATGTGGCGAGTAGGGTTGGACACAAATTCCTTGAGGATGGAACGAAGG
                 | | | ||  |  |          | ||   ||  | ||  |  || | |  | |||    |    |||   ||  | |      |||| ||| ||  ||||||||||| || || |||||||||||||||||||||||||| || ||  |||| || || |                                       
-----------------taatatttactgataaagaaaatgtataagcagaatagttgttcatgggtgtatatgttcaacaactaata-attttgggaaacattttttttaattccagATTGAAGGTCCTATCCACAGCTCAAATGTGATGCTCTACTCCAAAGATCAGAAGGTAGCAA---------------------------------------

upper sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv19s0014g04970.t01 (Vitis vinifera), 3'ss of exon 3
gtcagcattgtttctcttgaaacttctttctgtgctgcttctagctagtgtcgtatatatagtttcagatgcctgatcgttaacctatggttgttggtgttttctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAGAATGTGGCGAGTAGGGTTGGACACAAATTCCTTGAGGATGGAACGAAGG
      ||  |     | ||||| | |   |   |  |||  || ||     ||   | |   ||| |        || ||||    ||  | ||    |  |  || | ||||||||||  || || |||||||||||||||||||||||||| || ||| |||||||||| ||  |||| || || ||| |||| ||| ||||||     |
-----gatcctaaacatggaaacatgtgctt---cctctttaagttatgtgggttcttgtttcttctgtgattaagtcattaa----tgagtatttaaataatgattta-cagATTGAAGCGCCTATCCACAGCTCAAATGTGATGCTCTACTCCAAAGAACAGAATGTGGCTAGCCGGGTAGGTCATAAAATCCTAGAGAATGGAAAACGCG

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|88963467|gb|CI028482.1|CI028482
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|55412128|gb|CV724504.1|CV724504
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAG
EST: gi|88513297|gb|CI440803.1|CI440803
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88491612|gb|CI428884.1|CI428884
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|89171097|gb|CI040374.1|CI040374
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88471316|gb|CI408587.1|CI408587
EST:     GAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: GAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|33815049|gb|CF333389.1|CF333389
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88963128|gb|CI026801.1|CI026801
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|33815051|gb|CF333390.1|CF333390
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|55412138|gb|CV724514.1|CV724514
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|38474567|gb|CF958700.1|CF958700
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|55412137|gb|CV724513.1|CV724513
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAG
EST: gi|58594789|gb|CF993097.1|CF993097
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|86525540|gb|CI165746.1|CI165746
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|86833077|gb|CI333676.1|CI333676
EST:     AACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|89171939|gb|CI040449.1|CI040449
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88983366|gb|CI028602.1|CI028602
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88835407|gb|CI005097.1|CI005097
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|86416868|gb|CI030879.1|CI030879
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|33801796|gb|CF326771.1|CF326771
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88965734|gb|CI006617.1|CI006617
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|38477056|gb|CF961189.1|CF961189
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGACAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|86420528|gb|CI056517.1|CI056517
EST:     AGTCCAAGCACAAGAAAGGTACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|87028743|gb|CI349462.1|CI349462
EST:     AGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATCCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|55413199|gb|CV725575.1|CV725575
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAG
EST: gi|89169148|gb|CI038655.1|CI038655
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|55413200|gb|CV725576.1|CV725576
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|86881013|gb|CI339250.1|CI339250
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88955781|gb|CI092070.1|CI092070
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|86485533|gb|CI128166.1|CI128166
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88258084|gb|CI360670.1|CI360670
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88988439|gb|CI037676.1|CI037676
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|58689320|gb|CK078007.1|CK078007
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTAGTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|163920604|gb|EG710655.1|EG710655
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCT
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCT
EST: gi|38481942|gb|CF966007.1|CF966007
EST:     GTCCAAGCACAAGAAAGGAACAGAAGATGAGGCCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: GTCCAAGCACAAGAAAGGAACAGAAGATGA-ACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
EST: gi|88983464|gb|CI017696.1|CI017696
EST:     AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATG                         ATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG
genomic: AGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAG

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: 39 (upstream exon), 41 (downstream exon)
Score: 10

GCGGCTTTTTAAGCACAACAGCACTGTAATAGTGAAGGACTTGAACTTGAAGTCCAAGCACAAGAAAGGAACAGAAGATGAACCGGGTGAAATCGTCATGgtcagcattg ... ctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAGAATGTGGCGAGTAGGGTTGGACACAAATTCCTTGAGGATGGAACGAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtttcagatgcctgatcgttaacctatggttgttggtgttttctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAGAATGTGGCGAGTAGGGTTGGACACAAATTCCTTGAGGATGGAACGAAGG
                   cgttaac  putative branch site (score: 10)
                                       tgttttcttt  putative PPT
                                         ttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagcattgtttctcttgaaacttctttctgtgctgcttctagctagtgtcgtatatatagtttcagatgcctgatcgttaacctatggttgttggtgttttctttgatcagATTGAAGGCCCCATTCACAGCTCAAATGTGATGCTCTACTCAAAGGAAAAGAATGTGGCGAGTAGGGTTGGACACAAATTCCTTGAGGATGGAACGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA