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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatacggctgtattagttgggatattggttttgtcattgctggatgcacagccttttacggtgcgtttgctttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTGCATCCCTGTTACAAGTAAGGGACAACAAAGCAATTTGTTGTCTCTTTAT

Basic information

species Oryza sativa
transcript LOC_Os03g20310.1
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|88425762|gb|CI569349.1|CI569349
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88407487|gb|CI586328.1|CI586328
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|218492876|gb|FG956101.1|FG956101
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88383961|gb|CI631851.1|CI631851
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGACGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88352990|gb|CI630168.1|CI630168
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGACGCCTTACCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88345102|gb|CI628356.1|CI628356
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGACGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88332679|gb|CI660197.1|CI660197
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|66916817|gb|CX103665.1|CX103665
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88305366|gb|CI630528.1|CI630528
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGACGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88345518|gb|CI629779.1|CI629779
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGACGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|29658760|gb|CB655035.1|CB655035
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|5803454|gb|AI978424.1|AI978424
EST:     CCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: CCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|58591209|gb|CF989517.1|CF989517
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88449999|gb|CI572130.1|CI572130
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88432234|gb|CI565267.1|CI565267
EST:     ATCCAACGTGTACAGTTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATATCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|29658674|gb|CB654949.1|CB654949
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
EST: gi|88299315|gb|CI572267.1|CI572267
EST:     ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAA                         AGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG
genomic: ATCCAACGTGTACAGCTAATTTGATCTGTTGGCGCCTTAGCTAGAAgtaaggatac ... tttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttgtcattgctggatgcacagccttttacggtgcgtttgctttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTGCATCCCTGTTACAAGTAAGGGACAACAAAGCAATTTGTTGTCTCTTTAT
                                            ctttgat  putative branch site (score: 5)
                                        tttgcttt  CT-rich tract
                            tttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatacggctgtattagttgggatattggttttgtcattgctggatgcacagccttttacggtgcgtttgctttgatgtagAGGTGGCGACTCTGGCATCTCAGTGATCATAGGGCATTTGAAGGTGGCCTGCATCCCTGTTACAAGTAAGGGACAACAAAGCAATTTGTTGTCTCTTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA