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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagacagtagggaatatatgaacttcatactaatatatggccacagctctagggttttagaaactttttttctcataacattatgttttctaaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTTGTTGTTGATAGCAACGACAGAGATCGTGTGGTTGAGGCAAGGGATGAAC

Basic information

species Oryza sativa
transcript LOC_Os01g16030.3
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|88341576|gb|CI641328.1|CI641328
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|163929379|gb|EG713804.1|EG713804
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88341662|gb|CI641414.1|CI641414
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88339997|gb|CI650444.1|CI650444
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|66915825|gb|CX102673.1|CX102673
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88305327|gb|CI653053.1|CI653053
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|396941528|gb|HO188737.1|HO188737
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|163929270|gb|EG711031.1|EG711031
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88570756|gb|CI662129.1|CI662129
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88357962|gb|CI650698.1|CI650698
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88760986|gb|CI770542.1|CI770542
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|38476217|gb|CF960350.1|CF960350
EST:     AATAC-AGAACA-TAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGGTCTCATCTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAA-GGTCTCATCTT
EST: gi|88349175|gb|CI678148.1|CI678148
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88572261|gb|CI663832.1|CI663832
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88369043|gb|CI677620.1|CI677620
EST:     AATACAAGAACATTACCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCACAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88742204|gb|CI765712.1|CI765712
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
EST: gi|88454148|gb|CI693823.1|CI693823
EST:     AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG                         ATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT
genomic: AATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAGgtaaaaacca ... taaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctagggttttagaaactttttttctcataacattatgttttctaaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTTGTTGTTGATAGCAACGACAGAGATCGTGTGGTTGAGGCAAGGGATGAAC
                                          ttctaaa  putative branch site (score: 2)
                                      tgttttct  CT-rich tract
         ttttagaaactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagacagtagggaatatatgaacttcatactaatatatggccacagctctagggttttagaaactttttttctcataacattatgttttctaaactacagATCAGACCTTTGTGGAGGCACTATTTCCAGAACACTCAAGGTCTCATCTTTGTTGTTGATAGCAACGACAGAGATCGTGTGGTTGAGGCAAGGGATGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC