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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATGATAATGTCACTACTGGTGTCATATGCCATGGAGAGAAGAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtgacatacataatcaacatacctttttgtcccgttgtgcctttggtaaatattgacttgtacattatcatagagatgaaaatcatatattcc...

Basic information

species Oryza sativa
transcript LOC_Os09g13870.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g13870.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G050658_T03 (Zea mays), 5'ss of exon 5
GTTTATGATAATGTCACTACTGGTGTCATATGCCATGGAGAGAAGAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtgacatacataatcaacatacctttttgtcccgttgt-gcctttggtaaatattgacttgtacattatcatagagatgaaaatcatatattcc
|||||||||||  | ||||||||||| |||||| |||||| |||||| || ||||| ||||| |||||||||||||| || || |||  |||||||||||  || |||| |  |   |  |||     |   | ||     | | || |   | ||   |||  |  | |  || |  ||     ||  |||   
GTTTATGATAACATTACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACAGTTCATgtaagtaatgtcata-accacataagtactcaaatagtctgtaaccacgtatgttctttgttatattgatccctttggtacacttgttgcccaactatgga

upper sequence: LOC_Os09g13870.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G024615_T05 (Zea mays), 5'ss of exon 6
GTTTATGATAATGTCACTACTGGTGTCATATGCCATGGAGAGAAGAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtgacatacataatcaacatacctttttgtcccgttgt-gcctttggtaaatattgacttgtacattatcatagagatgaaaatcatatattcc
|||||||||||  ||||||||||||| |||||| |||||| |||||| || ||||| ||||| |||||||||||||| || || ||| ||||||||||||  || |||| |  ||  |  |||     |  |  || |   | | || |     |||   | |  || ||  |  |  ||     ||  |     
GTTTATGATAACATCACTACTGGTGTTATATGCAATGGAGTGAAGAGCGTAATCAAGGAAGGCCACAAGAGCTTTCCCAGTGGACACACTTCATgtaagtaatggcata-accatataagtactcaaatagcgtgtagccacatatgttctcctttgtaatattgatcatggtgcacttgttgcccaactccatg
















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|33666578|gb|CF297545.1|CF297545
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
EST: gi|88693827|gb|CI735330.1|CI735330
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
EST: gi|29642303|gb|CB647310.1|CB647310
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
EST: gi|88691322|gb|CI733906.1|CI733906
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGG
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGG
EST: gi|29640276|gb|CB645285.1|CB645285
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
EST: gi|29642638|gb|CB647645.1|CB647645
EST:     GAGTGTCATCCAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGG
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGG
EST: gi|29671233|gb|CB667508.1|CB667508
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
EST: gi|300215590|gb|HO088216.1|HO088216
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
EST: gi|88691866|gb|CI733443.1|CI733443
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
EST: gi|88690889|gb|CI734968.1|CI734968
EST:     GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCAT                         GGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA
genomic: GAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtg ... acaactccagGGTCTTTTGCTGGTCTAGGCTTCCTTGCATGGTACTTAGCTGGGAAGATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATGATAATGTCACTACTGGTGTCATATGCCATGGAGAGAAGAGTGTCATCAAAGAAGGTCACAAGAGCTTTCCAAGCGGGCACTCTTCATgtaagtggtgacatacataatcaacatacctttttgtcccgttgtgcctttggtaaatattgacttgtacattatcatagagatgaaaatcatatattcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT