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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaaatattactgttagacagatgagagatagtttttcatttttgaaataatgcttgtaaagagagcaaatcaagttactgtttttctttgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG

Basic information

species Oryza sativa
transcript LOC_Os01g16030.2
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|88339997|gb|CI650444.1|CI650444
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88694598|gb|CI738636.1|CI738636
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88760986|gb|CI770542.1|CI770542
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88570416|gb|CI661789.1|CI661789
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88353172|gb|CI654438.1|CI654438
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88357962|gb|CI650698.1|CI650698
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|163929270|gb|EG711031.1|EG711031
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|117234117|gb|CT842356.1|CT842356
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88302447|gb|CI668293.1|CI668293
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88347834|gb|CI635927.1|CI635927
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88453678|gb|CI683368.1|CI683368
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88341662|gb|CI641414.1|CI641414
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88454148|gb|CI693823.1|CI693823
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88341576|gb|CI641328.1|CI641328
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88454038|gb|CI691003.1|CI691003
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88570756|gb|CI662129.1|CI662129
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88410309|gb|CI575907.1|CI575907
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88735809|gb|CI757384.1|CI757384
EST:     CTCTACAAGCCTCAAGCTTGGAGAGATTGTCCCCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: CTCTACAAG-CTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|2310839|gb|C26994.1|C26994
EST:     TNTCTACANGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACANGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88572261|gb|CI663832.1|CI663832
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88742204|gb|CI765712.1|CI765712
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88734570|gb|CI758078.1|CI758078
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88349175|gb|CI678148.1|CI678148
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88305327|gb|CI653053.1|CI653053
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|163929379|gb|EG713804.1|EG713804
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88572018|gb|CI663589.1|CI663589
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88664650|gb|CI700897.1|CI700897
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88369043|gb|CI677620.1|CI677620
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTACCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88571110|gb|CI662483.1|CI662483
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|66915825|gb|CX102673.1|CX102673
EST:     TCTCTACAAGCTCAAGCTTGGAGAGACTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88762783|gb|CI772339.1|CI772339
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|88333173|gb|CI641016.1|CI641016
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
EST: gi|396941528|gb|HO188737.1|HO188737
EST:     TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAG                         GGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG
genomic: TCTCTACAAGCTCAAGCTTGGAGAGATTGTCACCACCATTCCAACAATAGgtaaaaacct ... tgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaataatgcttgtaaagagagcaaatcaagttactgtttttctttgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG
                                          ctttgat  putative branch site (score: 5)
                               ttactgtttttcttt  CT-rich tract
                                     tttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaaatattactgttagacagatgagagatagtttttcatttttgaaataatgcttgtaaagagagcaaatcaagttactgtttttctttgatgtctagGGTTTAATGTGGAGACTGTTGAATACAAGAACATTAGCTTCACTGTCTGGGATGTCGGGGGTCAAGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
gcaaaata
- - - - -tactgtt
- - - - - - - - - - - - - - - - - -tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - -atgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagcaaa