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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtttgctcgtgttgctgccag

Basic information

species Oryza sativa
transcript LOC_Os11g33240.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 1
-----------------------------GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtttgctcgtgttgct-gccag-----------------------------
                                |    |   |  |||| |||||||||||||||||||| |||||||| |||||  | |||||||||||||||||||| ||||   | |  ||     | || | |   |  | | ||| | || | ||| | |||||    || |||  |  | |  |  ||| |                             
TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcggtggcgctttgtc----cttcacggccggtcgtgt-tgcgtgtgggctgtcgtgctgatgagccttttttttttctcccccgcccgactcccgtgctgttcgtacgtgttgccag

upper sequence: LOC_Os11g33240.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 3
-------------GTC-CACCCCTGCAGGC-GGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagt--ggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtt-tgctcgtgttgctgccag
             ||   | ||  ||   | ||| |||||||||||||||||||| |||||||| |||||| | ||||||||||||||||||  |  | | | |  |      | |||| |  |   |||   | ||  | ||| ||      |      ||  | ||||  |  || ||||||
CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttccgtttagcggtgtcgctttgtccttcaccggtttagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccag

upper sequence: LOC_Os11g33240.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 2
----------GTC-CACCCCTGCAGGC-GGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagt--ggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtt-tgctcgtgttgctgccag
          ||   | ||  ||   | ||| |||||||||||||||||||| |||||||| |||||| | ||||||||||||||||||  |  | | | |  |      | |||| |  |   |||   | ||  | ||| ||      |      ||  | ||||  |  || ||||||
TGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttccgtttagcggtgtcgctttgtccttcaccggtttagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccag

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|88342082|gb|CI644419.1|CI644419
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|44677691|gb|CR291125.1|CR291125
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88424666|gb|CI606465.1|CI606465
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88389277|gb|CI598075.1|CI598075
EST:     TGGGGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGA
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGA
EST: gi|88718825|gb|CI742335.1|CI742335
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|117245193|gb|CT843395.1|CT843395
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88391585|gb|CI600774.1|CI600774
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88396101|gb|CI595649.1|CI595649
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88370889|gb|CI595001.1|CI595001
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88718610|gb|CI742120.1|CI742120
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88368924|gb|CI635234.1|CI635234
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|86902238|gb|CI302269.1|CI302269
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88729100|gb|CI752610.1|CI752610
EST:     TGGCGTCCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCACATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88439183|gb|CI604468.1|CI604468
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGG
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGG
EST: gi|88422482|gb|CI571464.1|CI571464
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|33793807|gb|CF322790.1|CF322790
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|86900894|gb|CI304099.1|CI304099
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|86901424|gb|CI308405.1|CI308405
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88727820|gb|CI749332.1|CI749332
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88352129|gb|CI613780.1|CI613780
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88352215|gb|CI613866.1|CI613866
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCAAAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
EST: gi|88315947|gb|CI618823.1|CI618823
EST:     TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT
genomic: TGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGT

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: 47 (upstream exon), 63 (downstream exon)
Score: 6

GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtg ... ttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtttgctcgtgttgctgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT