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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtacacggtttggttttgcatattattcagttcattttggcaagcccaaagcttctttgagacatttccgtatgtattgtatttgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG

Basic information

species Oryza sativa
transcript LOC_Os02g58580.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G017365_T09 (Zea mays), 3'ss of exon 7
gtaggtacacggtttggttttgcatattattcagttcattttggcaagcccaaagcttctttgagacatttccgtatgtattgtatttgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG
    ||| ||     ||  |    || |  |   ||   ||    |||   |||      || ||||   |  | | ||  |  |  |  || ||||||  |||| || || ||||| || |||||||| ||||||||||| ||||||||||| |||||||| || ||||||||||||  |||  ||
----gtaaacaa---ggcctcaggtagtcgttcatttggttcaaaaag---aaaatgcacttaagacgcatgagcaagtgataga--tattctccagATTGCTGCTTGTGAAGATGTCTCCGAAGTATGGCAAGGTCGATTCTGGGAGCTTGTTCCTGGTCAGGCAGTTGGATCTCTCTCCATTAGG

upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G491551_T01 (Zea mays), 3'ss of exon 1
gtaggtacacggtttggttttgcatattattcagttcattttggcaagcccaaagcttctttgagacatttccgtatgtattgtatttgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG
     ||  |  ||    |  |    | ||||| ||  ||    |||    |||      || ||||   |  | | ||  |  |  |  || | ||||   ||| ||  | ||||| | |||||| || |||||||||||||||| |||||| ||||||||  | | ||||||||||  |||| ||
-----taagcaattc--ctcaggtcgtcattcatttggtt----caaaaagaaaatgcacttaagacgcatgagcaagtgataga--tattctctagattgttgcttgtaaagATGTCTTTGAAGTGTGGCAAGGTCGATTTTGGGTGCTTGTTCCTGGTCAGACAGGTGGATCTCTCTCCATCAGG
















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|88487175|gb|CI424446.1|CI424446
EST:     TACCAGGTGCTTCAGACAG                         ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
genomic: TACCAAGTGCTTCAGACAGgtaggtacac ... tgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
EST: gi|86887374|gb|CI313277.1|CI313277
EST:     CTCTTACCAAGTGCTTCAGACAG                         ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
genomic: CTCTTACCAAGTGCTTCAGACAGgtaggtacac ... tgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
EST: gi|88486200|gb|CI423471.1|CI423471
EST:     TACCAGGTGCTTCAGACAG                         ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
genomic: TACCAAGTGCTTCAGACAGgtaggtacac ... tgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
EST: gi|86507803|gb|CI150436.1|CI150436
EST:     TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAG                         ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
genomic: TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAGgtaggtacac ... tgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
EST: gi|86862201|gb|CI330735.1|CI330735
EST:     TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACC-AGTGCTTCAGACAG                         ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
genomic: TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAGgtaggtacac ... tgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
EST: gi|8858691|gb|AU096009.1|AU096009
EST:     TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAG                         ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
genomic: TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAGgtaggtacac ... tgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
EST: gi|29661174|gb|CB657449.1|CB657449
EST:     TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAG                         ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
genomic: TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAGgtaggtacac ... tgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
EST: gi|89170146|gb|CI039423.1|CI039423
EST:     TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAG                         ATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG
genomic: TTGCACCAGGCAATGTGCCACCTTCAGCTCTTACCAAGTGCTTCAGACAGgtaggtacac ... tgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaagcccaaagcttctttgagacatttccgtatgtattgtatttgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG
                                           tttgctc  CT-rich tract
                                tatgtattgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtacacggtttggttttgcatattattcagttcattttggcaagcccaaagcttctttgagacatttccgtatgtattgtatttgctcaccagATAACTGCGTGCGAGGATGTTTCTGAAGTATGTCAAGGTCGATTTTGGGAGCTTGTACCTGGTCACGCTGTTGGATCTCTCGACATCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT