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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcaagtaaagatgtctgaaacatactgatatgtcaatcagggctggcatcaacatgatcaggatttatttatttatttatttatttatttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os04g59494.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 18
aatgcaagtaaagatgtctgaaacatactgatatgtcaatcagggctggcatcaacatgatcaggatttattta-----tttatttatttatttatttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG
     || || |    | || |   |  ||   | ||   || || |  |   || ||| |||      || |      || | |   |||| | |    |||||||  |||||||||||||| | |||||||| || ||||| ||||| || |||||||||||||||||||| || ||  ||||||||
----taattagaagattttgtacagttttggattttcgcccaaggttttc-ctaagatgctcatatacaatattgggacttcaatgccttatgtttaatcttcagGCATTGGGACCAGGATTTGCTCAGTTTGCGGAACCAGTGTTTCAAAGGTGCATCAATCTTATCCAATCGCAACAGTTGGCAAAG
















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|29626307|gb|CB631318.1|CB631318
EST:     CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAG                         GCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
genomic: CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAGgtacttacag ... tttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
EST: gi|29623086|gb|CB628097.1|CB628097
EST:     CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAG                         GCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
genomic: CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAGgtacttacag ... tttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
EST: gi|58611878|gb|CK039590.1|CK039590
EST:     CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAG                         GCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
genomic: CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAGgtacttacag ... tttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
EST: gi|58660018|gb|CK048698.1|CK048698
EST:     CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAG                         GCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
genomic: CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAGgtacttacag ... tttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
EST: gi|58667508|gb|CK056194.1|CK056194
EST:     CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAG                         GCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
genomic: CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAGgtacttacag ... tttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
EST: gi|58666235|gb|CK054921.1|CK054921
EST:     CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAG                         GCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
genomic: CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAGgtacttacag ... tttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
EST: gi|58662883|gb|CK051569.1|CK051569
EST:     CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAG                         GCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC
genomic: CTGATAAAGATTTATTCCCACTGCTCGAATGCTTTACATCTATCGCTCAGgtacttacag ... tttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggcatcaacatgatcaggatttatttatttatttatttatttatttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG
                                             tttatttc  CT-rich tract
              atcaggatttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgcaagtaaagatgtctgaaacatactgatatgtcaatcagggctggcatcaacatgatcaggatttatttatttatttatttatttatttatttcagGCCCTGGGACCAGGATTTTCACAGTTTGCTGAGCCAGTATTTCAGAGATGCATCAATCTTATCCAATCTCAGCACCTGGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG