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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagagctgtattgtctgtgtttttcatctaatcatcttcccttcttttctgttattcatgcaaattctcgactctaatgaaacgaaacttgtgtttgcagCTTTTTGTGGAGACGCAGATGTTCTCTGTTCTATCAGATTCTCGACTTTCCACATTTGAGAATGAACTAACATAAAACGGTTTGCTCTAGTCAGAGATCA

Basic information

species Oryza sativa
transcript LOC_Os03g05200.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05200.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G107651_T01 (Zea mays), 3'ss of exon 14
cagagctgtattgtctgtgtttttcatctaatcatcttcccttcttttctgtt--attcatgcaaattctcgactctaatgaaacgaaacttgtgtt--tgcagCTTTTTGTGGAGACGCAGATGTTCTCTGTTCTATCAGATTCTCGACTTTCCACATTTGAGAATGAACTAACATAAAACGGTTTGCTCTAGTCAGAGATCA--
       || ||  | ||    |   | |  |  | ||   ||  |  ||| |  |||  | |    | | | ||  | |   |  |  |||    |  ||||||| |||||||||||||||||||| ||||||||||||||||||||||| ||||  || || |||||||  |||||||  |  ||| || |||  |||||||  
----tgcgtgtttccagtagaatcagttttttttttttttttttgtcgctgctgtattttttccccattttgcctgcattctcattattcttaacatggtgcagCTCTTTGTGGAGACGCAGATGTTTTCTGTTCTATCAGATTCTCGACTGTCCAGTTTCGAAAATGAACGGACATAAAG-GCATTGTTCCAGT-GGAGATCAAA
















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|29624630|gb|CB629641.1|CB629641
EST:     AAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG                         CTTTTTGTGGAGACGCAGATGTTCTCTGTTCTATCAGATTCTCGACTTTCC
genomic: AAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAGgtatttgtag ... gtgtttgcagCTTTTTGTGGAGACGCAGATGTTCTCTGTTCTATCAGATTCTCGACTTTCC
EST: gi|29614852|gb|CB619865.1|CB619865
EST:     AAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG                         CTTTTTGTGGAGACGCAGATGTTCTCTGTTCTATCAGATTCTCGACTTTCC
genomic: AAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAGgtatttgtag ... gtgtttgcagCTTTTTGTGGAGACGCAGATGTTCTCTGTTCTATCAGATTCTCGACTTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgttattcatgcaaattctcgactctaatgaaacgaaacttgtgtttgcagCTTTTTGTGGAGACGCAGATGTTCTCTGTTCTATCAGATTCTCGACTTTCCACATTTGAGAATGAACTAACATAAAACGGTTTGCTCTAGTCAGAGATCA
                          ctctaat  putative branch site (score: 3)
      ttattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagagctgtattgtctgtgtttttcatctaatcatcttcccttcttttctgttattcatgcaaattctcgactctaatgaaacgaaacttgtgtttgcagCTTTTTGTGGAGACGCAGATGTTCTCTGTTCTATCAGATTCTCGACTTTCCACATTTGAGAATGAACTAACATAAAACGGTTTGCTCTAGTCAGAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA