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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtacatggcagttcaaattatctgaataacaggatttcatattagtattatttaacacatgttaatcaatcataatatttctcctgtccacccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g05630.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
ggtacatggcagttcaaattatctgaataacaggatttcatattagtattatttaacacatgtta---atcaatcataatatttctcctgtc-cacccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTG
      || |   |   || | ||||||| ||||||| ||   ||      ||  ||   | ||    ||   |  | || |||  ||  || |     |||||| ||||| |||||||||||||||||||| || ||| |||||||||||||||||||||||||||| |||||||| || ||||||||||
---ttgtgacgaat-ggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
ggtacatggcagttcaaattatctgaa----taacaggatttcatattagtattatttaacacatgttaatcaatc-ataatatttctcctgtccacccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTG
| |  ||   | | ||  || ||  |     |  ||||||| ||   || |   |||    |||  | ||  | |  || || |||  ||  ||    | |||||||||||| |||||||||||||||||||| || ||| |||||||||| |||||||||||||| || |||||||| || ||||||||||
gctgaatcagaat-cagtttctcaaatcgtttgtcaggattccaatctaatcgcatt----acacttcaacaattttatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
















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|5003494|gb|AU068643.1|AU068643
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|29668036|gb|CB664311.1|CB664311
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|29639786|gb|CB644795.1|CB644795
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|29677669|gb|CB673944.1|CB673944
EST:     GTTGCTAATG-TGNGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GTTGCTAATGTTG-GAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|29666851|gb|CB663126.1|CB663126
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|29688008|gb|CB684283.1|CB684283
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|33680351|gb|CF308590.1|CF308590
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|163920197|gb|EG714431.1|EG714431
EST:     TTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: TTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|33675133|gb|CF303372.1|CF303372
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTATAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|29686520|gb|CB682795.1|CB682795
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACTAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|44671917|gb|CR285351.1|CR285351
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAAACCGAGCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|29640127|gb|CB645136.1|CB645136
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|29662047|gb|CB658322.1|CB658322
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
EST: gi|33681625|gb|CF309864.1|CF309864
EST:     GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATG                         CAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA
genomic: GGTTGCTAATGTTGGAGATTCTAGAGCAGTTGTTTGTAGAGGCGGGGATGgtaagtcact ... acccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattatttaacacatgttaatcaatcataatatttctcctgtccacccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTG
               tgttaat  putative branch site (score: 3)
                                 tttctcctgtccaccc  putative PPT
              atgttaatcaatcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtacatggcagttcaaattatctgaataacaggatttcatattagtattatttaacacatgttaatcaatcataatatttctcctgtccacccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA