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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttccattttgctccgttagctacctctgttcagaattggatttaacatttgatctaactaaatcaatcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAATCGCCCAGAAATTGACATAGGTCCAGAACTATCCAACTTGAAGGAATTCA

Basic information

species Oryza sativa
transcript LOC_Os02g57630.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57630.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G108739_T01 (Zea mays), 3'ss of exon 5
gttagttccattttgct------ccgttagctacctctgttcagaatt--ggatttaacatttgatcta-actaaatcaatcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAATCGCCCAGAAATTGACATAGGTCCAGAACTATCCAACTTGAAGGAATTCA
||||||||  || || |      || ||||||| |   |||    | |  |   |||||| |      | |     | | | | |  ||||||||| |||||||||||||||||||||||||||| ||| | |||||||||||||| ||||||||||| || |||||| ||||  | |||||||||||||
gttagttctgttctgtttctgtccctttagctaaccacgtttgctactctgtgcttaacaataacaggatatccttttacttattttcagGTCATCACTAATGCATGTGCTACTCAAGCTATTCTCTCAGTTCTCATGAATCGCCCTGAAATTGACATTGGCCCAGAATTATCTCAATTGAAGGAATTCA
















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|699770|gb|D46061.1|D46061
EST:     AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAG                         GTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
genomic: AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttcca ... tcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
EST: gi|29668373|gb|CB664648.1|CB664648
EST:     AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAG                         GTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
genomic: AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttcca ... tcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
EST: gi|25798730|gb|CA754699.1|CA754699
EST:     AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAG                         GTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
genomic: AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttcca ... tcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
EST: gi|699786|gb|D46077.1|D46077
EST:     AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAG                         GTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
genomic: AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttcca ... tcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
EST: gi|218484923|gb|FG943842.1|FG943842
EST:     AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAG                         GTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
genomic: AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttcca ... tcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
EST: gi|29668412|gb|CB664687.1|CB664687
EST:     AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAG                         GTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
genomic: AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttcca ... tcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
EST: gi|218495715|gb|FG959020.1|FG959020
EST:     AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAG                         GTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
genomic: AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttcca ... tcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
EST: gi|33797877|gb|CF324798.1|CF324798
EST:     AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAG                         GTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT
genomic: AACGGCCTGTCGTCAAAGATCCAAACCCAAACCTTTTCTTTGCTAGCCAGgttagttcca ... tcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctctgttcagaattggatttaacatttgatctaactaaatcaatcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAATCGCCCAGAAATTGACATAGGTCCAGAACTATCCAACTTGAAGGAATTCA
                                  aactaaa  putative branch site (score: 2)
                  atttaacatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttccattttgctccgttagctacctctgttcagaattggatttaacatttgatctaactaaatcaatcactgccagGTCATCCCTAATGCATGTGCTACTCAAGCTATTCTGTCAATCCTCATGAATCGCCCAGAAATTGACATAGGTCCAGAACTATCCAACTTGAAGGAATTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA