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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatcctaccatgcattttctgtctatgaaggtcatgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATTACTTTTTACAACCTGACATACCCATTGAATCGCAATTGGCATGTGTTGG

Basic information

species Oryza sativa
transcript LOC_Os10g21890.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g21890.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G028501_T01 (Zea mays), 3'ss of exon 7
gtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatcctaccatgcattttctgtctatgaaggtcatgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATTACTTTTTACAACCTGACATACCCATTGAATCGCAATTGGCATGTGTTGG
||||||| ||||| |||||| |         | | |||  ||||      |   | || || | |||  |           ||||   | || ||| |                   ||||||||  |||  ||| |||  |||   || || |||||||||||| || ||||||||||||||||| || |||||||||||  | |||||||| ||||||||||||||||| |||||||| | ||||||||| ||||
gtaagtagtggaatgagaaatgt-----actgctgattgcattgcctcgttgcatatagcccatcattta----------gtgaa---cctgtaatgaa------------------ttttgttg-tttcgcttactaatagaagacctatt-gcagAATGAGGACCGTAAGCTGTGGAAGCTGGGTACGCTGCCTCCAGGTTTAATTACTTTCTACAACCTGACATACCCGTTGAATCGTACTTGGCATGTCTTGG

upper sequence: LOC_Os10g21890.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv03s0038g03750.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatcctaccatgcattttctgtctatgaaggt-catgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgttt-gcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATTACTTTTTACAACCTGACATACCCATTGAATCGCAATTGGCATGTGTTGG
                                                     | | ||  | |||  ||        | | |||  | | | | |||  || |  |   || || |  ||  |   | |     | |     || | |||||| ||||||||| ||| | |  || ||||| || ||  |  |||| || |||||||| ||||| |||||||||||||| |||||| |||| |  |||||||||||||
-----------------------------------------------------gatgatttttccagtcacc------caaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG
















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|89184385|gb|CI046950.1|CI046950
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|88839947|gb|CI079401.1|CI079401
EST:     ATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: ATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|86481041|gb|CI123674.1|CI123674
EST:     TTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGGAAGCTGGGCACACTGCCTCCAGGACTGAT
genomic: TTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGT-GGAAGCTGGGCACACTGCCTCCAGGACTGAT
EST: gi|29622298|gb|CB627309.1|CB627309
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29625260|gb|CB630271.1|CB630271
EST:     AGTGGAAGAAGCAAAATATCCCTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29629402|gb|CB634411.1|CB634411
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29622321|gb|CB627332.1|CB627332
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29629341|gb|CB634352.1|CB634352
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|86479242|gb|CI121875.1|CI121875
EST:     AGTGGAAGAAGCGAAATATCACTGGGATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|86501675|gb|CI144308.1|CI144308
EST:     AGTGGAAGAAGCTAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29628619|gb|CB633630.1|CB633630
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|88966673|gb|CI365896.1|CI365896
EST:     AGCGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCACGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATTACTTTTTACAACCTGACATACCCATTGAATCGCAATTGGCATGTGTTGG
                            atttaat  putative branch site (score: 4)
                                          tttctgttt  putative PPT
      taatttatcttttgtt  TA-rich tract