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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccacgttatgttagaatctttgttcacgttccatagtacctgtatagtaagattatttagggttgttggacgtaactgagcgcttctgctttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTCAGAGTGTAGGATGGAAATCCTTTGATCTATTGGGAAAATAAATCAGGGC

Basic information

species Oryza sativa
transcript LOC_Os03g15120.1
intron # 16
splice site 3'
intron type U2

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|86504136|gb|CI146769.1|CI146769
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88227851|gb|CI227331.1|CI227331
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|89164031|gb|CI101119.1|CI101119
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88438607|gb|CI543711.1|CI543711
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88265787|gb|CI376689.1|CI376689
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88531682|gb|CI460092.1|CI460092
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATNCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|86600373|gb|CI356130.1|CI356130
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88907823|gb|CI091221.1|CI091221
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88515936|gb|CI443590.1|CI443590
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|87010113|gb|CI279210.1|CI279210
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88552745|gb|CI482783.1|CI482783
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|33808918|gb|CF330345.1|CF330345
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88978697|gb|CI385038.1|CI385038
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|86500063|gb|CI142696.1|CI142696
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88260746|gb|CI363039.1|CI363039
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|86432146|gb|CI085757.1|CI085757
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88221798|gb|CI221754.1|CI221754
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|86597766|gb|CI274757.1|CI274757
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|87016640|gb|CI275642.1|CI275642
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
EST: gi|88849245|gb|CI087767.1|CI087767
EST:     AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAG                         GTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC
genomic: AAACAAATGCTTCTGCTGCCCTTGCTGCTGGCATTTTCCATCGGAAAGAGgtattgtccc ... tttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtaagattatttagggttgttggacgtaactgagcgcttctgctttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTCAGAGTGTAGGATGGAAATCCTTTGATCTATTGGGAAAATAAATCAGGGC
                         acgtaac  putative branch site (score: 3)
                                      cttctgcttt  putative PPT
     agattattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccacgttatgttagaatctttgttcacgttccatagtacctgtatagtaagattatttagggttgttggacgtaactgagcgcttctgctttatcacagGTTCCGATTTCAGCAGTGAAAGAGCATCTGGTAGATGCTGGCGTGGAGGTCAGAGTGTAGGATGGAAATCCTTTGATCTATTGGGAAAATAAATCAGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - ttatgtt
- - - - - - - - - - - - - - - - - - gtacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgttg