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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgaacaccactcacctttgttcattagcatgtcataatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTTGAGCATGAGTACTTCAAGGACCTTGAGATGGTACAATGACCCTGCTATG

Basic information

species Oryza sativa
transcript LOC_Os03g01850.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 8
gtaagtcgaacaccactcacctt-tgttcattagcatgtcataatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTTGAGCATGAGTACTTCAAGGACCTTGAGATGGTACAATGACCCTGCTATG-
||||||| ||      ||   |  || |||| | |    ||| |||||   || |     |    | |    || |  ||| ||  |   ||| |||||||||||| |||| ||||||| |||||| ||||||||||| || || |||||||| ||||||||||||||||||||||||||||| ||||| |||||   
gtaagtcaaatggatttctgttgatgatcatgaccgctgcatcatatatatcctctctgtattgaatt----cacc--tgtttccgtctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACC-TGCTAAAT

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 7
gtaagtcgaacaccactcacctt-tgttcattagcatgtcataatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTTGAGCATGAGTACTTCAAGGACCTTGAGATGGTACAATGACCCTGCTATG-
||||||| ||      || |||  || ||||        | | ||| | ||| |    | || |  | || ||| |  | | ||  ||  ||| |||||||||||||| |||||||||| |||||| |||||||| || || || |||||||||||||||||||||||||||||  ||||||| ||||| |||||   
gtaagtcaaatggatttctcctgatgatcatggctgctgcttcatacatccctc----acagtattgaat-tcacc--tatttctgtttgctgacagAAAATGCTTCGATACGAGCCAAGCAAAAGAATCACAGCGAGGCAAGCACTTGAGCATGAGTACTTCAAGGACCTTGAAGTGGTACAGTGACC-TGCTAAAT
















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|33803869|gb|CF327809.1|CF327809
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88268788|gb|CI378723.1|CI378723
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|3766971|gb|AU031081.1|AU031081
EST:     TTGCAANTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|29662032|gb|CB658307.1|CB658307
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88446676|gb|CI526509.1|CI526509
EST:     GTCCCTACTCTTGACCCTGCTGG-TTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGGTAGACAGGCTCTT
genomic: GTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88559037|gb|CI489575.1|CI489575
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGNTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88253212|gb|CI351838.1|CI351838
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAAACAAAAAGGATCACAGCTAGACAGGCTC
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAA-CAAAA-GGATCACAGCTAGACAGGCTC
EST: gi|88978284|gb|CI384727.1|CI384727
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|86885548|gb|CI318699.1|CI318699
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCCGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|89196147|gb|CI397149.1|CI397149
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88437700|gb|CI531259.1|CI531259
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAAT-GCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCT
EST: gi|88488941|gb|CI426212.1|CI426212
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88509819|gb|CI437325.1|CI437325
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCANACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88437696|gb|CI531255.1|CI531255
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|38482398|gb|CF966438.1|CF966438
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|66915263|gb|CX102111.1|CX102111
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88522726|gb|CI450366.1|CI450366
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTTGAGCATGAGTACTTCAAGGACCTTGAGATGGTACAATGACCCTGCTATG
                                      tctcgtttc  CT-rich tract
             aaaaaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgaacaccactcacctttgttcattagcatgtcataatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTTGAGCATGAGTACTTCAAGGACCTTGAGATGGTACAATGACCCTGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG