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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtttacattttgcatggtgaaaacaagttacttttaaaagggtgcatttctgctgaattttcttcctatttttgagcaaacattattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT

Basic information

species Oryza sativa
transcript LOC_Os09g12660.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 5
gtaaggtttacattttgcatggtgaaaacaagttacttttaaaagggtgcatttctgctgaattttcttcctatttttgagcaaacattattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT
     || |   || | ||||   | |  ||||||      | | | |||| || | ||  || | |  | ||  ||||| ||||||||  ||| | |||||||||||| ||||||||  ||||||||||||||||| |||| |||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| 
-----gtatggtttgtacatgtctacataaagtta------agatgttgcaatttt-ctagatctaccacttacctttgatcaaacatt-ctgtatacagCTTCTATGATCGTTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGG

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
---------gtaag--gtttacattttgcatggtgaaaacaagttacttttaaaag-ggtgcatttctgctgaattttcttcctatttttgagcaaacat-tattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT
          || |   ||||   | | |||  |    |||| |   ||| ||  |  ||  |||   | |    | | |   | ||  ||          |||||  ||||| |||||||| |||||  |  |||| || || ||||| ||||| |||||||| || ||  | |||||||||||||| || || ||||||||||||||||| 
gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
gtaaggtttacattt------tgcatggtgaaaacaagt-tacttttaaaagggtgcatttctgctgaattttcttcctatttttgagcaaacat-tattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT
||||  |    ||||      | |||  |    |||| | || ||  |  |  |||  ||   | |    | | |   | ||  || |        |||||  ||||| |||||||| |||||  |  |||| || || ||||| ||||| |||||||| || ||  | |||||||||||||| || || ||||||||||||||||| 
gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatgatagtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------gtaaggtttacattttgcatggtgaaaacaagttacttttaaaagggtgcatttctgctgaattttcttcctatttttgagcaaacattattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT
                       |||   | |  ||||||     ||   |  |||| |||| |  |     |||||||| || | ||| |     |  |   |     |   |    ||||||||||| ||||||||  |  |||| || || ||||||||||| ||||| ||||| ||  | |||||||||||||| || || |||||||||||||| || 
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcatta--ccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaaggtttacattttgcatggtgaaaacaagttacttttaaaagggtgcatttctgctgaattttcttcctattt-ttgagcaaacattattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT
    |   |||  ||      || || | |   |    |   |    ||  |||    |||  ||||| | ||     |         || ||   ||||| || || ||| | ||  |  | ||||| || ||  |||||| | | |||||||||||| |  | || ||||||||||| |||||||||||||| ||||||
-attgacatactgttccagcagtaaagaaataattgaatctgagtattgtgtttggaatgatatttctgcttaaccactttttttcttttgtttcctgcagTTTTTACGACAGGTCGTCTCCTATTTACACACAGGCTCGATTCCTTCCTCCATCAAAAATGTTGGACGCTGATGTGACTGACAGTGTTATTGGAGAAGGT

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|86858990|gb|CI275175.1|CI275175
EST:     TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|24468914|gb|CA305863.1|CA305863
EST:     TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|86517463|gb|CI157669.1|CI157669
EST:     TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|58683758|gb|CK072445.1|CK072445
EST:     AACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: AACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|29675781|gb|CB672056.1|CB672056
EST:     TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|218485015|gb|FG946141.1|FG946141
EST:     ACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: ACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|88232188|gb|CI230646.1|CI230646
EST:     TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|86520775|gb|CI160981.1|CI160981
EST:     TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|86500004|gb|CI142637.1|CI142637
EST:     TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACNTCGATACTTGCCTCC
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|86504994|gb|CI147627.1|CI147627
EST:     TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAG                         CTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCC
EST: gi|58674587|gb|CK063274.1|CK063274
EST:     TTCTACAATGCCAACTTGGGGATAACCGAGAAACCTGTGCCAGATTTTAG                         CTGCTATGACCGTTCTGCCGCAATTTATACG
genomic: TTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATTTTAGgtaaggttta ... ttgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgcatttctgctgaattttcttcctatttttgagcaaacattattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT
                                     aaacattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtttacattttgcatggtgaaaacaagttacttttaaaagggtgcatttctgctgaattttcttcctatttttgagcaaacattattgtgtgcagCTTCTATGACCGTTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT