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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagatagatataactgatcccatatgtaggacttgctagttgattgtattgtttaccaaaaatccaaaatccataattgatttgaaactgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCATTCGGCCACAGCTGTTGGAGCTGAGCTGACCCACAGCTTCTCGAGCAAC

Basic information

species Oryza sativa
transcript LOC_Os09g19734.1
intron # 5
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|33680951|gb|CF309190.1|CF309190
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|29634623|gb|CB639632.1|CB639632
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|84117435|gb|CD151202.1|CD151202
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCATCATTGAACCT                         GAACAACAAGGGAGACAGTCTCACTGCATCTTATTACCACATT
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATT
EST: gi|33827852|gb|CF339741.1|CF339741
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|427625|gb|D23758.1|D23758
EST:     GCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: GCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|58587649|gb|CF985957.1|CF985957
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCATCATTGAGCCT                         GAACAACAAGGGAGACAGTCTCACTGCATCTTATTACCACATTGTGAACC
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACC
EST: gi|33802112|gb|CF326928.1|CF326928
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|163920092|gb|EG709862.1|EG709862
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|33827932|gb|CF339781.1|CF339781
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GA-CAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|163927455|gb|EG709935.1|EG709935
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|33794658|gb|CF323216.1|CF323216
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAA-AACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
EST: gi|33825589|gb|CF338605.1|CF338605
EST:     AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCT                         GAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA
genomic: AATGCTGGATTGAGCTTCAGTAATGATGATCTTATCGCGTCATTGAACCTgtaagtgtct ... tgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtattgtttaccaaaaatccaaaatccataattgatttgaaactgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCATTCGGCCACAGCTGTTGGAGCTGAGCTGACCCACAGCTTCTCGAGCAAC
                               aattgat  putative branch site (score: 4)
                                            ctgtctt  putative PPT
                             ataattgatttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagatagatataactgatcccatatgtaggacttgctagttgattgtattgtttaccaaaaatccaaaatccataattgatttgaaactgtcttgcagGAACAACAAGGGAGATAGTCTCACTGCATCTTATTACCACATTGTGAACCATTCGGCCACAGCTGTTGGAGCTGAGCTGACCCACAGCTTCTCGAGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA