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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgtcttgctctttatcaaccatagcaattaacaggattacatgaattgcaataatggttataattttgcaattctaattgcagATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAGATAATACTATTTTTGAAGCAGATCCCACGAGCCTTGGCACTGCAGCATA

Basic information

species Oryza sativa
transcript LOC_Os05g16824.1
intron # 16
splice site 3'
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|88852433|gb|CI374201.1|CI374201
EST:     TTTCCGAGGATCTCCAGAAT                         ATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAG
genomic: TTTCCGAGGATCTCCAGAATgtatatgtct ... ctaattgcagATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAG
EST: gi|33677441|gb|CF305680.1|CF305680
EST:     TCTAGGCTGCCTCCAACAAGACACTCCTTGTTTCCGAGGATCTCCAGAAT                         ATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAG
genomic: TCTAGGCTGCCTCCAACAAGACACTCCTTGTTTCCGAGGATCTCCAGAATgtatatgtct ... ctaattgcagATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAG
EST: gi|58687444|gb|CK076131.1|CK076131
EST:     TCTAGGCTGCCTCCAACAAGACACTCCTTGTTTCCGAGGATCTCCAGAAT                         ATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAG
genomic: TCTAGGCTGCCTCCAACAAGACACTCCTTGTTTCCGAGGATCTCCAGAATgtatatgtct ... ctaattgcagATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacaggattacatgaattgcaataatggttataattttgcaattctaattgcagATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAGATAATACTATTTTTGAAGCAGATCCCACGAGCCTTGGCACTGCAGCATA
                                           ttctaat  putative branch site (score: 2)
                             ttataattttgcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgtcttgctctttatcaaccatagcaattaacaggattacatgaattgcaataatggttataattttgcaattctaattgcagATTACTCCTTCGCAGTTGACTGCGGCAGTAATAGTTCTACGAGTGCCTCAGATAATACTATTTTTGAAGCAGATCCCACGAGCCTTGGCACTGCAGCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG