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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaacttacttgctatccttcttcagggaattatacctaactttttaagtcatttgaactttgaaaccaatctaaaattgacgcttctccttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG

Basic information

species Oryza sativa
transcript LOC_Os01g14140.1
intron # 1
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|88412635|gb|CI690381.1|CI690381
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAG                         GAAGCACCATTCGACTTGCTGAGGGACAG
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... cttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG
EST: gi|325494157|gb|JG458681.1|JG458681
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAG                         GAAGCACCATTCGACTTGCTGAGGGACAG
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... cttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG
EST: gi|88851563|gb|CI671003.1|CI671003
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAG                         GAAGCACCATTCGACTTGCTGAGGGACAG
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... cttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG
EST: gi|86260931|gb|CI066606.1|CI066606
EST:     GGCTTGTGCTCCTCTACTTCTCCTCAG                         GAAGCACCATTCGACTTGCTGAGGGACAG
genomic: GGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... cttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG
EST: gi|88571066|gb|CI662439.1|CI662439
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTC--                         --AGCACCATTCGACTTGCTGAGGGACAG
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... cttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG
EST: gi|88741066|gb|CI764574.1|CI764574
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAG                         GAAGCACCATTCGACTTGCTGAGGGACAG
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... cttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG
EST: gi|163927940|gb|EG713516.1|EG713516
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAG                         GAAGCACCATTCGACTTGCTGAGGGACAG
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... cttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG
EST: gi|66913626|gb|CX100474.1|CX100474
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAG                         GAAGCACCATTCGACTTGCTGAGGGACAG
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... cttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagtcatttgaactttgaaaccaatctaaaattgacgcttctccttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG
                               aattgac  putative branch site (score: 3)
                                     cgcttctccttttcac  CT-rich tract
                        aatctaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaacttacttgctatccttcttcagggaattatacctaactttttaagtcatttgaactttgaaaccaatctaaaattgacgcttctccttttcacagGAAGCACCATTCGACTTGCTGAGGGACAG

- - - -tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - tcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccaa