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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTTTCCATTGATGAAATTAAATTAACACCTCTGGAGCTTTCTGAATTGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgcctctatttcttctgactgttgtttctgtactgaatatgatggccaggactgagttttgactgttcttattatttctatctggagataggc...

Basic information

species Oryza sativa
transcript LOC_Os11g34210.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g34210.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G091560_T01 (Zea mays), 5'ss of exon 5
AAAACTTTCCATTGATGAAATTAAATTAACACCTCTGGAGCTTTCTGAATTGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc----ctctatttcttc--tgactgttgtttctgtactgaatatgatg-gccaggactgagttttgactgttcttattatttctatctggagataggc----------------------------------
|||| | ||||||||||||||||||||||||||||| |||||||||||| |||| ||||| || | |||||||||||| ||||||||||| || |||||||||   ||||    ||   ||||  |  |   |  ||||| |   ||  || |  || |    ||| |  | | |  | | |  |||  |    | || |    |                                    
AAAAGTATCCATTGATGAAATTAAATTAACACCTCTAGAGCTTTCTGAACTGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgctaaactgggtttccccccttgttactgtttttcagctctatgttctgagttttgacagtctatagggtctacacatttctaggctttgcaccctgattgatgacaaagcctctctaaatctgtccttgcag
















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|88901789|gb|CI374397.1|CI374397
EST:     TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|29616532|gb|CB621544.1|CB621544
EST:     TGATTGCATCTATAAAGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|58606373|gb|CK034406.1|CK034406
EST:     TGATTGCATCTATAAAGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|3760962|gb|C98216.1|C98216
EST:     TTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|89175846|gb|CI042867.1|CI042867
EST:     TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|89181776|gb|CI113282.1|CI113282
EST:     GTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: GTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|86493642|gb|CI136275.1|CI136275
EST:     TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|86839311|gb|CI331559.1|CI331559
EST:     TGATTGCATCTATAAGGAAT-GAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCCAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|86498082|gb|CI140715.1|CI140715
EST:     TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|89169673|gb|CI110032.1|CI110032
EST:     CAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: CAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|29646032|gb|CB651039.1|CB651039
EST:     TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|29641132|gb|CB646139.1|CB646139
EST:     TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
EST: gi|86834558|gb|CI344489.1|CI344489
EST:     TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAG                         ATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG
genomic: TGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc ... gtccttgcagATTCTGATTGAACTCATTGCGAAAGGTGGAACTGTCAAGTCTGTGATAGAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACTTTCCATTGATGAAATTAAATTAACACCTCTGGAGCTTTCTGAATTGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgcctctatttcttctgactgttgtttctgtactgaatatgatggccaggactgagttttgactgttcttattatttctatctggagataggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG