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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCACTTGGTCCTCCCAGCTCACTCACCTCAGTTTACACAGGCTAGTGGTTCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctgtctggactgctgttatcttttcttgtgattatctggtagtaactgttctttttctgtccctaatag

Basic information

species Oryza sativa
transcript LOC_Os02g48340.2
intron # 6
splice site 5'
intron type U2

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|29645024|gb|CB650031.1|CB650031
EST:     TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAG                         GTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
genomic: TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctg ... tccctaatagGTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
EST: gi|58674908|gb|CK063595.1|CK063595
EST:     GCTGAACTATGCTGCCAAACATTTGTACCTTGAG                         GTACCCTTAGATTGCAGCAGGACGAAAGAGCAGTGCTGCTGTATTTGTAGT
genomic: GCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctg ... tccctaatagGTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
EST: gi|33793822|gb|CF322799.1|CF322799
EST:     TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAG                         GTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
genomic: TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctg ... tccctaatagGTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
EST: gi|58676595|gb|CK065282.1|CK065282
EST:     TCAGACCCAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAG                         GTACCCTTAGATTGCAGCAGGACCAAAGAGCAGTGCTGCTGTATTTGTAGT
genomic: TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctg ... tccctaatagGTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
EST: gi|38479722|gb|CF963811.1|CF963811
EST:     TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAG                         GTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
genomic: TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctg ... tccctaatagGTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
EST: gi|29677295|gb|CB673570.1|CB673570
EST:     TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAG                         GTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGGAGT
genomic: TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctg ... tccctaatagGTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
EST: gi|218479580|gb|FG967759.1|FG967759
EST:     TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAG                         GTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
genomic: TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctg ... tccctaatagGTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
EST: gi|33676574|gb|CF304813.1|CF304813
EST:     TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAG                         GTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT
genomic: TCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctg ... tccctaatagGTACCCTTAGATTGCAGCAGGACAAAAGAGCAGTGCTGCTGTATTTGTAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCACTTGGTCCTCCCAGCTCACTCACCTCAGTTTACACAGGCTAGTGGTTCAGACCAAAGAGCAAGCTGAACTATGCTGCCAAACATTTGTACCTTGAGgtttgttctgtctggactgctgttatcttttcttgtgattatctggtagtaactgttctttttctgtccctaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC