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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggcatagtctccaaagcgaggatgtactaatgcatatattttgttttgccttcatttgactaaaatatacgatagttaacttgtaccttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTATTGCATGAACGACCCTAGCCCAAGTTTCCACGGTCTGCCAATGAGCAGCT

Basic information

species Oryza sativa
transcript LOC_Os02g25580.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 17
attggcatagtctccaaagcga--ggatgtactaatgcatatattttgttttgccttca--tttgactaaaatatacgatagttaacttgtaccttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTATTGCATGAACGACCCTAGCCCAAGTTTCCACGGTCTGCCAATGAGCAGCT
         ||  | |  || |  ||   |  | ||     |||||      | |   |  |||||||   ||  ||  |  || | || |    |||   |||||  | || || || |||||||| |||||||| |||||||| || | |   || ||||||||||| |||||||||||||||||     |          |
---------gtaccaatcgcaattggccttgttgattttcctatttgcacaggacactacttttgactttgatg-actttttttcatttctggtatttgc-cagGAACTCATCGAAAAACTTAGCAAAGGAGAATTGCCAAAAGAGGATTTCCCATGTATGAACGACCCAAGCCCAAGTTTCCACGGATCAACCTCACTTTCAT
















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|29626795|gb|CB631806.1|CB631806
EST:     CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAG                         GACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
genomic: CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAGgtataaatat ... ttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
EST: gi|38481465|gb|CF965554.1|CF965554
EST:     CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAG                         GACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
genomic: CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAGgtataaatat ... ttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
EST: gi|218485563|gb|FG949368.1|FG949368
EST:     CTGGGGAAGAATCTACATGGGCACTTACCCGATTTTATCCTGTTCTAGAG                         GACTTGATTGAGAAGCTT
genomic: CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAGgtataaatat ... ttttatacagGACTTGATTGAGAAGCTT
EST: gi|29626796|gb|CB631807.1|CB631807
EST:     CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAG                         GACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
genomic: CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAGgtataaatat ... ttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
EST: gi|29626758|gb|CB631769.1|CB631769
EST:     ACTTTCCCGATTTTATCCTGTTCTAGAG                         GACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
genomic: ACTTTCCCGATTTTATCCTGTTCTAGAGgtataaatat ... ttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
EST: gi|29689435|gb|CB685710.1|CB685710
EST:     CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAG                         GACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
genomic: CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAGgtataaatat ... ttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
EST: gi|86831700|gb|CI301550.1|CI301550
EST:     CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAG                         GACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
genomic: CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAGgtataaatat ... ttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
EST: gi|66914840|gb|CX101688.1|CX101688
EST:     CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAAAG                         GACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT
genomic: CTGGGGAAGAATCTACATGGGCACTTTCCCGATTTTATCCTGTTCTAGAGgtataaatat ... ttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgccttcatttgactaaaatatacgatagttaacttgtaccttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTATTGCATGAACGACCCTAGCCCAAGTTTCCACGGTCTGCCAATGAGCAGCT
                                         tacctttt  CT-rich tract
           atttgactaaaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggcatagtctccaaagcgaggatgtactaatgcatatattttgttttgccttcatttgactaaaatatacgatagttaacttgtaccttttatacagGACTTGATTGAGAAGCTTAGCAAGGGAGAATTACCAAAAGACGAATACTATTGCATGAACGACCCTAGCCCAAGTTTCCACGGTCTGCCAATGAGCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT