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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcaaaagcaatttctttgtcgtgttattttgaatatgtctagaccaataattgtacttactgagtgcttgttgatagcgttcattttctctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTACCACCTAAACGGGGGATCACACAGTACCATCCAATCCATTAGATCAGTC

Basic information

species Oryza sativa
transcript LOC_Os03g02850.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G171469_T03 (Zea mays), 3'ss of exon 4
----------------------------------------------------ctgcaaaagcaatttctttgtcgtgttattttgaatatgtcta---gaccaataattgtacttactgag--tgcttgttgatagcgttcattttctctttg-gcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTACCACCTAAACGGGGGATCACACAGTACCATCCAATCCATTAGATCAGTC
                                                      |     | | || |||||| ||   | || ||     | ||   |  |  |  ||| |||| || |   |  ||  || | | | ||  ||      || |||| |||  ||||||| ||| ||| |||||||||||||||| ||||||||||| || || |  || |||||  |||| |||||||||||||||||| |     
gtatgttttttattcaaataaattgtttgtgcaggtttagagttaatagtgtgcgtctttggacttactttgtggtaccaattagatctcttatatatggtcggtcgttgcacttgctcatattcttttctgttggtgctcccttgtgacctgtgcagCTGGCCGAGATTGCACCCTCATCTTTGGTGCTGTTCATCTTAAGGAAACTGCCGCCAAGGCGTGGGATTGCACAATACCATCCAATCCATTAGTTTGTCT
















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|88825029|gb|CI775594.1|CI775594
EST:     CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
genomic: CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
EST: gi|29659764|gb|CB656039.1|CB656039
EST:     CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
genomic: CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
EST: gi|86413919|gb|CI068126.1|CI068126
EST:     CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
genomic: CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
EST: gi|88450172|gb|CI541933.1|CI541933
EST:     CCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
genomic: CCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
EST: gi|29664030|gb|CB660305.1|CB660305
EST:     CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
genomic: CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
EST: gi|89168924|gb|CI020464.1|CI020464
EST:     ATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
genomic: ATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
EST: gi|88735360|gb|CI758868.1|CI758868
EST:     CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
genomic: CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
EST: gi|86498594|gb|CI141227.1|CI141227
EST:     ATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
genomic: ATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA
EST: gi|41881458|gb|BX927423.1|BX927423
EST:     CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTG                         TTGGTTGAGATTGTACCTTCAGCTTTGGTGCTTTTCATATTAAGGAAACTA
genomic: CCGATCTTGATGTTCTGAACCATCCAATCCTAAACTTCTTCTACTACTTGgtatgtcttc ... tctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaataattgtacttactgagtgcttgttgatagcgttcattttctctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTACCACCTAAACGGGGGATCACACAGTACCATCCAATCCATTAGATCAGTC
                                  cgttcattttctcttt  CT-rich tract
                                    ttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcaaaagcaatttctttgtcgtgttattttgaatatgtctagaccaataattgtacttactgagtgcttgttgatagcgttcattttctctttggcagTTGGTTGAGATTGTACCTTCAGCTTTGGTGCTGTTCATATTAAGGAAACTACCACCTAAACGGGGGATCACACAGTACCATCCAATCCATTAGATCAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA