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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcctgcacccagaacactgtgcatattctaggtgtggatgacaatgagctgatgatgctttcatcagAGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGAATGTGGAGTCCCCTACGAGTCCTACTTCCCCATGCCTGCTTCCGGTAGG

Basic information

species Oryza sativa
transcript LOC_Os01g58640.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G326625_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------gtga-ttcctgcacccagaacactgtgcatattctaggtgtggatgacaatgagctgatgatgctttcatcagAGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGAATGTGGAGTCCCCTACGAGTCCTACTTCCCCATGCCTGCTTCCGGTAGG
                                                      |||| ||         | |  | |    ||||  |           |  |||| ||||||||| || |  ||| || || |     |||| ||| || |||  ||| || |||||||| || |||||||| ||  ||||||| || ||||||||||||||||||    ||| |
gtgaatttctttattcaaaagaatctttcacttctagtgcaattttcagtaatagtgaatttacagggtgatataaataaatatataatgcacaattgctatcatgaactgatgatggttcc-ccagGGATTACGTGAACTCTGCATCTGTTTATGTGACTCCTGATTCAGGGGGTGAATGTGGGGTTGCCTACGAATCATACTTCCCCATGCCTGCTGTTAGTAAG

upper sequence: LOC_Os01g58640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G138756_T02 (Zea mays), 3'ss of exon 7
------------------------------------------------------gtgattcctgcacccagaacactgtgcatattctaggtgtggatgaca--atgagctgatgatgctttcatcagAGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGAATGTGGAGTCCCCTACGAGTCCTACTTCCCCATGCCTGCTTCCGGTAGG
                                                      |||| |  | ||    ||      |  |||| | | |      ||  |  |||| ||||||||| || |  ||| || || ||  | |||| ||| || |||  ||| || |||||||| || |||||||| ||  ||||||| || ||||||||||||||||||    ||| |
gtgaatttctttattcaaaagaatctttcacttccagtgcaattttcagtaatagtgaatt-tacagggtgatataaataaatatacaatgcacaattgctatcatgaactgatgatggttcc-ccagGGATTACGCGAGCTCTGCATCTGTGTATGTGACTCCTGATTCAGGGGGTGAATGTGGGGTTGCCTACGAATCATACTTCCCCATGCCTGCTGTTAGTAAG
















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|29681233|gb|CB677508.1|CB677508
EST:     CCGCTCGCGTCGCAGGTGTCCTACATGACCGCCATTGGTAACCACGAGAG                         AGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGA
genomic: CCGCTCGCGTCGCAGGTGTCCTACATGACCGCCATTGGTAACCACGAGAGgtgattcctg ... ctttcatcagAGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGA
EST: gi|4714991|gb|AU056108.1|AU056108
EST:     CCGCTCGCGTCGCAGGTGTCCTACATGACCGCCATTGGTAANCACGAGAG                         AGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGA
genomic: CCGCTCGCGTCGCAGGTGTCCTACATGACCGCCATTGGTAACCACGAGAGgtgattcctg ... ctttcatcagAGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacactgtgcatattctaggtgtggatgacaatgagctgatgatgctttcatcagAGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGAATGTGGAGTCCCCTACGAGTCCTACTTCCCCATGCCTGCTTCCGGTAGG
                                  agctgat  putative branch site (score: 4)
                                             ctttcatc  putative PPT
          atattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattcctgcacccagaacactgtgcatattctaggtgtggatgacaatgagctgatgatgctttcatcagAGACTATGCAGGATCTGGATCGGTATATCCGACGCCGGATTCAGGCGGCGAATGTGGAGTCCCCTACGAGTCCTACTTCCCCATGCCTGCTTCCGGTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG