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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtttcattttgatgcctttagtcctgaatttgcatgttcggtgccaggatcattatgtaacaagcgcaacgattcatctcagagaagaactac...

Basic information

species Oryza sativa
transcript LOC_Os01g10150.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G045259_T02 (Zea mays), 5'ss of exon 13
GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtttcattttgatgcctttagtcctgaatttgcatgttcggtgccaggatcatt---atgtaacaagcgcaacgattcatctcagagaagaactac
|||||||||||||| |||||||||||||||| |||||| ||| |  |||||||| | ||||||||||||||  ||||||| ||||||| |||||   |  |    | | || |   | | | |   ||||  |  || |  | ||  || ||    ||   |     | |||  |   |    | || | |   
GAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattacat--ggtatcatccaggttgccttccgtttgtttcatctgccctagcctctttcccgtgctgcggattccacggctgtgcgttcacaacacccg-
















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|87040610|gb|CI195232.1|CI195232
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|396941388|gb|HO188597.1|HO188597
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|29645032|gb|CB650039.1|CB650039
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|89184391|gb|CI046956.1|CI046956
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|87024182|gb|CI256923.1|CI256923
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|29632066|gb|CB637075.1|CB637075
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|27546382|gb|CA764550.2|CA764550
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|29688779|gb|CB685054.1|CB685054
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|29626995|gb|CB632006.1|CB632006
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|29670786|gb|CB667061.1|CB667061
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|89195193|gb|CI051306.1|CI051306
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|89192726|gb|CI050024.1|CI050024
EST:     CGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCTATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: CGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|29670785|gb|CB667060.1|CB667060
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|86483807|gb|CI126440.1|CI126440
EST:     CTTTGGCTGGTTCAAATAATGGAAGCTCGNTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: CTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|88849770|gb|CI001476.1|CI001476
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|86483022|gb|CI125655.1|CI125655
EST:     TTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|58611769|gb|CK039481.1|CK039481
EST:     TCGTTGGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TC-TTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|3766584|gb|AU030694.1|AU030694
EST:     TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: TTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
EST: gi|87024232|gb|CI256973.1|CI256973
EST:     CTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG                         GAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA
genomic: CTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtt ... tgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAGgtatacagtttcattttgatgcctttagtcctgaatttgcatgttcggtgccaggatcattatgtaacaagcgcaacgattcatctcagagaagaactac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cggtgcc