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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatatgacacgtcaaaactttacactcctggatctaaacatccccttagacattttagcatattctcggtctcaatccatatttgatgcatgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACTGATGGTCAAATACGGATTTGAGTACTGCACTTCGCAAGCGATTCTTCAA

Basic information

species Oryza sativa
transcript LOC_Os05g51790.1
intron # 28
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|58659113|gb|CK047793.1|CK047793
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGTTAAAG                         CCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
EST: gi|86844639|gb|CI338619.1|CI338619
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTTAGAAGCCAGCTAAAG                         CCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
EST: gi|25798012|gb|CA753973.1|CA753973
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAG                         CCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
EST: gi|66914986|gb|CX101834.1|CX101834
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAG                         CCTGGAGCACCGGTGATATGCTGGAGAACAGTAATGAGCGTGAGTGGGCAC
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGAT-TGCTGGAGAACAGTAATGAGCGTGAGTGGGCAC
EST: gi|88845942|gb|CI084672.1|CI084672
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAG                         CCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
EST: gi|88418527|gb|CI504151.1|CI504151
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAG                         CCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
EST: gi|86418226|gb|CI032435.1|CI032435
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAG                         CCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
EST: gi|29628420|gb|CB633431.1|CB633431
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAG                         CCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
EST: gi|427226|gb|D23308.1|D23308
EST:     CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAG                         CCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT
genomic: CAGCATCCTAAATATCATGAATGGCCCATGGATTGAGAAGCCAGCTAAAGgtaatatgtg ... tgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagacattttagcatattctcggtctcaatccatatttgatgcatgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACTGATGGTCAAATACGGATTTGAGTACTGCACTTCGCAAGCGATTCTTCAA
                                   atttgat  putative branch site (score: 5)
                                 atatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatatgacacgtcaaaactttacactcctggatctaaacatccccttagacattttagcatattctcggtctcaatccatatttgatgcatgctttgcagCCTGGAGCACCGGTGATTGCTGGAGAACAGTAATGAGCGTGAGTGGGCACTGATGGTCAAATACGGATTTGAGTACTGCACTTCGCAAGCGATTCTTCAA

- - - - - - - - - - - - ctcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgca