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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatagccagaatgttttgatagctttcctgtctaatatgtcttgcatctgtttcgaactttgttttagtcactgatatacacatttttcatctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACATCAGCATAGTGCAAATCCGTTTGCAAACTCAAGCATCCAACCCTCAGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g40690.2
intron # 2
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|8860125|gb|AU097443.1|AU097443
EST:     CGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGGAGNTAATGATCCACATGTTTCCCCCAGAGTACA
genomic: CGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTAT-GGAGGTAATGATCCACATGTTTCCCCCAGAGTACA
EST: gi|8858461|gb|AU095779.1|AU095779
EST:     GGCTCACGGCGNCTGATATAATGTCTCATATCCAG                         CATGGAGTTGGATTATGGAGGTAATGATCCCACATGTTTCCCCCAGAGTAC
genomic: GGCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCAT-GAGTTGGATTATGGAGGTAATGAT-CCACATGTTTCCCCCAGAGTAC
EST: gi|8858452|gb|AU095770.1|AU095770
EST:     GCTCACGGCGGCTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: GCTCACGGCGGCTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
EST: gi|218492762|gb|FG946015.1|FG946015
EST:     CTGATATAATGTCTCATATCCAG                         CATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT
genomic: CTGATATAATGTCTCATATCCAGgttcaacctt ... tctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgtttcgaactttgttttagtcactgatatacacatttttcatctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACATCAGCATAGTGCAAATCCGTTTGCAAACTCAAGCATCCAACCCTCAGCTG
                        cactgat  putative branch site (score: 3)
                                    catttttcatcttt  putative PPT
                             atatacacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatagccagaatgttttgatagctttcctgtctaatatgtcttgcatctgtttcgaactttgttttagtcactgatatacacatttttcatctttgacagCATGAGTTGGATTATGGAGGTAATGATCCACATGTTTCCCCCAGAGTACATCAGCATAGTGCAAATCCGTTTGCAAACTCAAGCATCCAACCCTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - -tgttttg
- - - - - - - - - - - - - cctgtct
- - - - - - - - - - - - - - - - - - - -tcttgca
- - - - - - - - - - - - - - - - - - - - - - - -ctgtttc