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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTATGGATCACTGCTACAATTCAGAAGTGTTCGGTGATGACAACTGGTACAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctaccttgtgcctttttaattctgactatatcagaaataattgatatgaaaataaactggaaaactgatgcaagttttctatcttgtgaatgatgtcatctctgtacattacag

Basic information

species Oryza sativa
transcript LOC_Os04g57210.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57210.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G043862_T01 (Zea mays), 5'ss of exon 10
TGTATGGATCACTGCTACAATTCAGAAGTGTTCGGTGATGACAACTGGTACAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctaccttgtgcctttt-taattctga----ctatatcagaaataattgatatgaaaataaac-tggaaaactgat--gcaa-gttttctatcttgtgaatgatgtcatctctgtacattacag-------------------
|||||||||||||||||   ||||| |  | | |||||||||| |||||||||||| ||  ||||| | ||||| || || ||||| ||||||||| ||||||   |  | | ||| |  | ||  |||||    || | |      || ||| ||| |||| |||  ||||| | ||||  | || | | | |||  |  ||   || | || |  ||   | |  |                   
TGTATGGATCACTGCTATGTTTCAGGAACGGTTGGTGATGACAGCTGGTACAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtac-ttttcctatgcataatataggtctgatatactctttagatgttacttggtatcaaaacaaaaatggaataatgattggtaatgctatttattcta-gatctattttatttgggtcactgatggatatcatgtaatacaacag
















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|87033311|gb|CI187935.1|CI187935
EST:     GATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: GATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29626709|gb|CB631720.1|CB631720
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29663904|gb|CB660179.1|CB660179
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29663905|gb|CB660180.1|CB660180
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29618214|gb|CB623226.1|CB623226
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29626176|gb|CB631187.1|CB631187
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29679980|gb|CB676255.1|CB676255
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTTTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29624048|gb|CB629059.1|CB629059
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|58589122|gb|CF987430.1|CF987430
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29671067|gb|CB667342.1|CB667342
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29663603|gb|CB659878.1|CB659878
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29679981|gb|CB676256.1|CB676256
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTTTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTATGGATCACTGCTACAATTCAGAAGTGTTCGGTGATGACAACTGGTACAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctaccttgtgcctttttaattctgactatatcagaaataattgatatgaaaataaactggaaaactgatgcaagttttctatcttgtgaatgatgtcatctctgtacattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA