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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgttatgcatgcattagtattttctagaacacaatataaataattgagctatatcgaaggctagaagtttggtgacatggactgttttttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGCTTGAGAGAGAATGAAGGGCCATTGAAGAAGTTTGAGCAGGCTGCTTCCA

Basic information

species Oryza sativa
transcript LOC_Os01g05070.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05070.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G037134_T04 (Zea mays), 3'ss of exon 6
tgatgtt--atgcatgcattagtattttctagaacacaatataaataattgagctatatcgaaggctagaagtttggtgacatggactgttttttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGCTTGAGAGAGAATGAAGGGCCATTGAAGAAGTTTGAGCAGGCTGCTTCCA
  ||  |  | | | ||  || | |||| |       |  ||   | |  ||     |    ||  |       ||   | ||  ||  | ||| |   ||||||||||||||||||||||| |||||| | || |||||| ||||||| ||||||| |||||| ||||||||  ||||||| || ||  | ||| | ||||
-catactgaaggaaggccataatcttttttgttggtaaggatttgtcac-gactggcaaattagtttccttcactgaaaaaatcaacactgtttgtcttcagGCAAAGTTGCGGAGTTCTTCATGGTGGACACGGTACTTTGTCCAGACCGGCTTGACAGAGAACGAAGGGCCGCTGAAGAAATTCGAAGATGCTACATCCA

upper sequence: LOC_Os01g05070.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G011031_T01 (Zea mays), 3'ss of exon 6
tgatgttatgcatgcattagtatttt-ctagaacacaatataaataattgagctatatcgaaggctagaagttt--ggtgacatggactgttttttttca----cagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGCTTGAGAGAGAATGAAGGGCCATTGAAGAAGTTTGAGCAGGCTGCTTCCA
         || ||  || |  ||   ||  | |  |    |  || |||   |     | |   ||||   ||    |||||    ||   ||| ||      ||||||||  |||||||||| ||||||||| |  |||||||| ||||||||||||| | |||||| ||||||||| ||||||| |||||  ||||| | ||| 
-------tggcttgtgttgggtttcaactctagcctacccaaggtatttgtcatggccggcaaattagattctttcactgacaaaatctacctttgtttgtgtccagGCAAAACTGCGGAGTTCCTCGTGGTGGACAAGATACTTTGTCCAGACTGGCTTAACAGAGAACGAAGGGCCACTGAAGAAATTTGAAGAGGCTACATCCC
















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|89171249|gb|CI109773.1|CI109773
EST:     AGGTTTCTGAACTACCGAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
genomic: AGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|27546786|gb|CA767261.2|CA767261
EST:     CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
genomic: CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|88990961|gb|CI108348.1|CI108348
EST:     CTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGTTCTCGATACTTTATCCAGACTGGC
genomic: CTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|86496195|gb|CI138828.1|CI138828
EST:     CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
genomic: CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|88967189|gb|CI392145.1|CI392145
EST:     CTGAACTACCAAAATTC-GAAGACCG                         GCAAAGGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGG
genomic: CTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAA-GTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGG
EST: gi|88588825|gb|CI706667.1|CI706667
EST:     CAGGTCAACAGAAGGCTAAGGTTCCTGAACTACCAAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTCCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
genomic: CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|58586280|gb|CF984588.1|CF984588
EST:     CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
genomic: CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|218478522|gb|FG957886.1|FG957886
EST:     CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCANAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
genomic: CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|58674474|gb|CK063161.1|CK063161
EST:     CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTT
genomic: CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTT
EST: gi|25803803|gb|CA759764.1|CA759764
EST:     CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
genomic: CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|300215765|gb|HO088391.1|HO088391
EST:     CAGGTCAACAAAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAAACTGGC
genomic: CAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC
EST: gi|88262627|gb|CI366401.1|CI366401
EST:     GGTCAACAGGAAGGGTAAGGTTTGTGAAGCTACCAAAATTCGTAAGACCG                         GCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGG
genomic: GGTCAACA-GAAGGCTAAGGTTTCTGAA-CTACCAAAATTCGGAAGACCGgtacgtatgg ... tttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgagctatatcgaaggctagaagtttggtgacatggactgttttttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGCTTGAGAGAGAATGAAGGGCCATTGAAGAAGTTTGAGCAGGCTGCTTCCA
                                       ctgttttttttcac  CT-rich tract
                                        tgtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgttatgcatgcattagtattttctagaacacaatataaataattgagctatatcgaaggctagaagtttggtgacatggactgttttttttcacagGCAAAGTTGCGGAGTTCTTCGTGGTGGTCGCGATACTTTATCCAGACTGGCTTGAGAGAGAATGAAGGGCCATTGAAGAAGTTTGAGCAGGCTGCTTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT