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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttccctgttctcacaagtagtgtattcaacatgatcatgcgattgaagctaatttgctttgtgttgatcctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G136296_T03 (Zea mays), 3'ss of exon 9
gtgggttccctgttctcacaagta---gtgtattca--------acatgatcatgcgattgaagctaatttgcttt-gtgttgatcctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA
||| ||      |||||  | |     |||||||||        |||| ||  |  ||| | | ||| |||  ||   ||||||||  |||  |||| ||||||||||| |||||||||||||| ||||| ||||||||  | ||||| || || |||||||| || ||||| ||||||||||| ||||||||||
gtgtgtcttacattctccgatgacagtgtgtattcatcatgttcacataattgtatgatagtaactattttttttccatgttgatctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGCAGTCCTTCAGCCGAACGTCGGGTTAATCTGTCAAGCATTA

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 8
gtgggttccctgttctcacaag-tagtgt--attca---------acatgatcatgcgattgaagctaatttgcttt-gtgttgatcctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA
||| ||    ||||| || | | ||||||  |||||         |||| ||  |  ||| | |  || |||  |||  |||||| |  |||| |||| ||||||||||| |||||||||||||| ||||| ||||||||  | ||||| || ||||||||||| || ||||| ||||||||||| ||||||||||
gtgtgtcttatgttcccagatgatagtgtctattcatcatgattcacataattgtatgatagtaaatatttttttttcatgttgacctcttcacagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGAAGTCCTTCAGCTGAACGTCGGGTTAATCTGTCAAGCATTA

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------------------------------------------------gtgggttccctgttctcacaagtagtgtattcaacatgatcatgcgattgaagctaatttgctttgtgttgatcctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA
                                                                                                                      || | |    | ||     |       |||||||  |  |||| |  || |  ||| ||   ||||   | ||| |||   |||| || |||||||| ||||| |||||||||||||||||||||||  |   ||| || || |||||    ||||| || || || || |||||||| ||||
gtaaaattttctctaaccattggtttatcccaaattaaaaaggatctcatggtgaataatatccctgaggatttggtttttgaccaaagccaatgacgttgtgtgatccacatatattgtagttgttgtattagtttatcccaaatattcaatct--tcattcatttaagtctattt---tttggacttatctttttccagGTGGTTGAGGTTGTTAGTGGAGATTGCATCATTGTTGCTGATGATTCGATTCCATATGGCAGTCCACTAGCAGAGCGGCGAGTCAACCTTTCAAGTATTA

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 9
--------------gtgggttccctgttctcacaagtagtgtattcaacatgatcatgcg--attgaagctaa--tttgctttgtgttgatcctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA
               ||    |  |||| |   |  |||| ||| | | ||| |||  |   ||| |   |||   ||  ||||   | ||| |||   |||| || |||||||| ||||| |||||||||||||||||||||||      ||| || || |||||    ||||| || || || || |||||||| ||||
gtggtccacatatattgtagacgttgttgttgtat-tagtttatcccaaatgttcaatcttcattcattttaagtctttttttggacttatctttttccagGTGGTTGAGGTTGTTAGTGGAGATTGCATCATTGTTGCTGATGATTTGATTCCGTATGGCAGTCCACTAGCAGAGCGGCGAGTCAACCTTTCAAGTATTA

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 8
----gtgggttccctgt----tctcacaagtagtgtattcaacatgatcatgcgattgaagctaatttgctttgtgttgatcctttcat----agGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA
    |||  ||  ||||    |      |  ||   ||      | |  |     || ||     ||   | | |    ||| |    |    ||||||| |||||||||||||| || |||||||||||||||||||| || |  || || || ||||| |  |||||||| || || ||||| ||||| || |
gtaagtgctttttctgtgaaattatttgacaaggtcatctctgttaactaaatacttaaatagtcttctatctttacacatcttcctgtctccagGTTGTGGAGGTTGTGAGTGGAGACTGCATCATTGTTGCTGATGATGCTGTCCCATATGGCAGTCCATTGGCAGAACGACGAGTCAATCTCTCAAGTATCA

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 9
-----------gtgggttccctgttctcacaagtagtgtattcaaca--tgatcatgcgattgaagctaatttgctttgtgttgatcctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA
           ||        || |  |  || |  | | ||  | |  ||    |       ||  | || | | |    ||   |||||  ||||| || |||||||| |||||||||||||||||||| ||||||||  |    || | ||| || || |  |||||||| || ||||| || || || || |
gtgggtagttggtcaacataatgcttacgtaaatcctatcttttataaatggaattttaccctaattttatgtccatctcatttggcctttt-tagGTGGTTGAGGTTGTAAGTGGGGATTGCATCATTGTAGCTGATGATTCTCTCCCATTCGGCAGCCCATTAGCAGAACGACGAGTTAACCTCTCCAGTATCA

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|29674463|gb|CB670738.1|CB670738
EST:     CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAA                         GTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGA
genomic: CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGA
EST: gi|29623577|gb|CB628588.1|CB628588
EST:     CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAA                         GTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
genomic: CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
EST: gi|58658629|gb|CK047309.1|CK047309
EST:     CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAA                         GTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGGTGATGACGCAGCT
genomic: CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
EST: gi|29625604|gb|CB630615.1|CB630615
EST:     CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAA                         GTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
genomic: CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
EST: gi|29656202|gb|CB652477.1|CB652477
EST:     CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAA                         GTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
genomic: CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
EST: gi|58684285|gb|CK072972.1|CK072972
EST:     CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAA                         GTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
genomic: CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
EST: gi|58606427|gb|CK034460.1|CK034460
EST:     ACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAGAG                         GGTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGC
genomic: ACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAA-AAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGC
EST: gi|29644258|gb|CB649265.1|CB649265
EST:     CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAA                         GTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
genomic: CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT
EST: gi|29623984|gb|CB628995.1|CB628995
EST:     CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAA                         GTTGTAGAGGTTGTGAGTGGGGATTGCATCATTTTTGCTGATGACGCAGCT
genomic: CACCAGTGACAAACTCGAAGCCAATCCACGACCAGAAATTCACTGGAAAAgtgggttccc ... cctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaacatgatcatgcgattgaagctaatttgctttgtgttgatcctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA
                                            tcctttcat  CT-rich tract
                          taattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttccctgttctcacaagtagtgtattcaacatgatcatgcgattgaagctaatttgctttgtgttgatcctttcatagGTTGTAGAGGTTGTGAGTGGGGATTGCATCATTGTTGCTGATGACGCAGCTCCTTACGGAAGTCCTTCTGCAGAACGCCGGGTTAATCTTTCAAGCATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG