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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggatataaaagagaccttgcttctttttaattacatgatcattattgtgatgactgcataactaacatctttttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACAAGATTCACCTGGACCAGTGACAAGGAGGCGCTTGGCTATGACTGAAGCA

Basic information

species Oryza sativa
transcript LOC_Os01g55090.1
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|86865592|gb|CI330997.1|CI330997
EST:     AA-GTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|29675819|gb|CB672094.1|CB672094
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|88483397|gb|CI420668.1|CI420668
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|88256058|gb|CI358446.1|CI358446
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|86540363|gb|CI180569.1|CI180569
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|86866361|gb|CI336957.1|CI336957
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|88517006|gb|CI444660.1|CI444660
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|86540334|gb|CI180540.1|CI180540
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattacatgatcattattgtgatgactgcataactaacatctttttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACAAGATTCACCTGGACCAGTGACAAGGAGGCGCTTGGCTATGACTGAAGCA
                                 aactaac  putative branch site (score: 1)
                                       catctttttttctt  CT-rich tract
                                    taacatcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggatataaaagagaccttgcttctttttaattacatgatcattattgtgatgactgcataactaacatctttttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACAAGATTCACCTGGACCAGTGACAAGGAGGCGCTTGGCTATGACTGAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC