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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgttttcacccaaatgagttatacttctcctgtccatgcatgtgctaaattatcttcaaaatagtagttctgtgcttaaccttgtatgattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG

Basic information

species Oryza sativa
transcript LOC_Os05g36110.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 1
------------ttctgttttcacccaaatgagttatacttctcctgtccatgcatgtgctaaattatcttcaaaatagtagttctgtgcttaaccttgtatgattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG
            || ||  | || |||||||| || |  ||| || | |      | |   |||  ||  ||  | |     |  |||        |  | ||||  || ||||||  ||||||||||||||||||||||||||||||||||||||||| |||||
actttcttgtttttttggatgcatccaaatgaattttgtttc-ccggacagaatttat-tcaaacaattctcgtagttaatatcttgt--------tcatttgat--aatagGCATTCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACTGGATG

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G048150_T03 (Zea mays), 3'ss of exon 1
---ttctgttttcacccaaatgagttatacttc--tcctgtccatgcatgtgctaaattatcttcaaaatagtagttctgtgcttaaccttgtatgattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG
   ||||   | ||||||||||| || |  ||   |||| | ||| ||||||| |   | ||     || |||  || |  ||| |    |  ||     || ||||||| ||||||||||||||||||||||||||||||||||||||||| |||||
tttttcttgatgcacccaaatgattttttttttgttcctctacattcatgtgccaggatttc----gaacagttcttgta-gctaatatcttcatttcataatagGCATGCTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACCGGATG
















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|29657648|gb|CB653923.1|CB653923
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|13896941|gb|AU183277.1|AU183277
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88740560|gb|CI764068.1|CI764068
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|1631723|gb|C19452.1|C19452
EST:     CGGTCAAGTCGCCGCCG-GGCCCACCTCGCCGGCGAACTCCACCCGCAA-                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88732124|gb|CI757301.1|CI757301
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88739463|gb|CI762971.1|CI762971
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|29621889|gb|CB626900.1|CB626900
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88759825|gb|CI769381.1|CI769381
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88739598|gb|CI763106.1|CI763106
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|58695852|gb|CK084539.1|CK084539
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88357088|gb|CI615975.1|CI615975
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88343606|gb|CI622981.1|CI622981
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|29621929|gb|CB626940.1|CB626940
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88745549|gb|CI768909.1|CI768909
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88762333|gb|CI771889.1|CI771889
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|87012610|gb|CI307358.1|CI307358
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
EST: gi|88413003|gb|CI578854.1|CI578854
EST:     GGTCAAGTCGCCGCCGCGGCCCACCTCGCCCGGCGAACTCCACCCGCAAG                         GCATGTTTTGCTGTTCTTCAAAAGCTGGGTGTCAAGAAAATTTATGACAGG
genomic: GGTCAAGTCGCCGCCGCGGCCCACCTCGCC-GGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAA-GCTGGGTGTCAAGAAAATTTATGACAGG
EST: gi|88732046|gb|CI757223.1|CI757223
EST:     CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAG                         GCATGTNTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA
genomic: CGGTCAAGTCGCCGCCGCGGCCCACCTCGCCGGCGAACTCCACCCGCAAGgtctagatcg ... gattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctaaattatcttcaaaatagtagttctgtgcttaaccttgtatgattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG
     aattatcttcaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgttttcacccaaatgagttatacttctcctgtccatgcatgtgctaaattatcttcaaaatagtagttctgtgcttaaccttgtatgattaaacagGCATGTTTTGCTGTTCTTCAAAGCTGGGTGTCAAGAAAATTTATGACAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG