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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCAACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtctttcttgtccctagtaaccttatacttgctaaaatgtgtaatattaagtgctgtaaaaaatgaatgctattctaccttattatttaatatcag...

Basic information

species Oryza sativa
transcript LOC_Os08g41460.6
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41460.8 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 3
CCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCAACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtctttcttgtcc--ctagtaaccttatacttgctaaaatgtgtaatattaagtgctgtaaaaaatgaatgctatt-ctaccttattatttaatatcag
||| |||||||| |  |||||||||||  ||||||| |||||  | ||||||||||| ||||| |||| |||||| ||| |||||||||||||| ||| |||| ||  |  ||  ||  ||   |||||| | || | |   |||  |  | | |  |||| || || | | |||      | |    |  |   || || | 
CCCAGATGAGCAGAAGCTTTTGGAAGCCGCCATGGCGTATGTCTCGGGCAACCCCATCATGACGGATGATGAATTCGATCAACTAAAGCTGAGACTAAAGgtttgttctcgttacccgcctgtgaaccttttgctag-tgcgatg-atggtgtgatatgctatataagaaggatggagcaacaagacgaccagagaaaataa-
















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|29625905|gb|CB630916.1|CB630916
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
EST: gi|58595312|gb|CF993620.1|CF993620
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
EST: gi|29684942|gb|CB681217.1|CB681217
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
EST: gi|38474705|gb|CF958838.1|CF958838
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
EST: gi|29662553|gb|CB658828.1|CB658828
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
EST: gi|29683115|gb|CB679390.1|CB679390
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
EST: gi|29663222|gb|CB659497.1|CB659497
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
EST: gi|163920678|gb|EG710011.1|EG710011
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
EST: gi|29615644|gb|CB620656.1|CB620656
EST:     ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGG                         AAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT
genomic: ACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtcttt ... tcttggccagAAAGAGGGAAGTGAAATCGTACAAGAAGGTCCAAGATGCAGTCTTCGAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTGATGAGCAAAGACTTTTGGAAGCATCCATGGCTTATGTGGCTGGCAACCCCATTATGACAGATGCTGAATTTGATGAACTAAAGCTGAGATTAAGGgttggtctttcttgtccctagtaaccttatacttgctaaaatgtgtaatattaagtgctgtaaaaaatgaatgctattctaccttattatttaatatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA