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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtaccatcacgatgtcgtcttcttgtttttgtgttcagaacttcagatgtttgagtttgtagctgactcttctgtttcttgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGACGAGCTCATGGCGGGAGGGTCGTCGGGTGACACTAGGATGGTGGCCATG

Basic information

species Oryza sativa
transcript LOC_Os01g39330.1
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|88342620|gb|CI656325.1|CI656325
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|87009604|gb|CI309125.1|CI309125
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGTTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88668071|gb|CI722810.1|CI722810
EST:     CGCCGCCGCCCGACCTCCACGACCCCCTC-TTCTGGCCGGCTTTCGCCGA                         CTGTGCTGNGAGCTTCATCGCCGGCGGCGGNGGCGACAATGCGTGCTTCGA
genomic: CGCCGCCGCCCGACCTCCACGACCCC-TCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88677165|gb|CI731278.1|CI731278
EST:     CCGNCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGNGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88594774|gb|CI714732.1|CI714732
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGNGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88593897|gb|CI713851.1|CI713851
EST:     CCGCCGNCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGNGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88672064|gb|CI726180.1|CI726180
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88671570|gb|CI725686.1|CI725686
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|2309818|gb|C25973.1|C25973
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGTTTCATCGCCGGCGGGGGCGGCGACAATACGTGTTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|29635867|gb|CB640876.1|CB640876
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88674395|gb|CI727406.1|CI727406
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88954437|gb|CI718416.1|CI718416
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88675886|gb|CI729458.1|CI729458
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88593862|gb|CI713816.1|CI713816
EST:     CCGC-GCCGCCCGACCTCCACGACCCCTCNTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGNGGCGACAATGCGTGCTTNGA
genomic: C-GCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88687950|gb|CI731526.1|CI731526
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGNGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88954952|gb|CI720301.1|CI720301
EST:     CCGCCGCCGCCCGACCTCCACCACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88675354|gb|CI729467.1|CI729467
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGNGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
EST: gi|88744297|gb|CI767657.1|CI767657
EST:     CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGA                         CTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA
genomic: CCGCCGCCGCCCGACCTCCACGACCCCTCCTTCTGGCCGGCTTTCGCCGAgtacgtacca ... tgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagaacttcagatgtttgagtttgtagctgactcttctgtttcttgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGACGAGCTCATGGCGGGAGGGTCGTCGGGTGACACTAGGATGGTGGCCATG
                          agctgac  putative branch site (score: 3)
                                ctcttctgtttcttgt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtaccatcacgatgtcgtcttcttgtttttgtgttcagaacttcagatgtttgagtttgtagctgactcttctgtttcttgtatctcagCTGTGCTGCGAGCTTCATCGCCGGCGGCGGCGGCGACAATGCGTGCTTCGACGAGCTCATGGCGGGAGGGTCGTCGGGTGACACTAGGATGGTGGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG