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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttgtttaccttgctcttctgaagttctgatattgtactagaattcttgtatagtatttctctcatcatctttacagCTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGCCAACATGTTATCTTCCAAGCCCTGCACATGGGCTGTCTCCAATCTCCAT

Basic information

species Oryza sativa
transcript LOC_Os12g03720.2
intron # 2
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|33676109|gb|CF304348.1|CF304348
EST:     CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAG                         CTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
genomic: CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAGgttcttgttt ... atctttacagCTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
EST: gi|33675029|gb|CF303268.1|CF303268
EST:     CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAG                         CTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
genomic: CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAGgttcttgttt ... atctttacagCTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
EST: gi|33675459|gb|CF303698.1|CF303698
EST:     CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAG                         CTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
genomic: CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAGgttcttgttt ... atctttacagCTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
EST: gi|33674757|gb|CF302996.1|CF302996
EST:     CCGGCGATGAGTTCTTGGTCGTCC-CAATGGCATCATCACAAACTACGAG                         CTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
genomic: CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAGgttcttgttt ... atctttacagCTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
EST: gi|33675346|gb|CF303585.1|CF303585
EST:     CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAG                         CTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC
genomic: CCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAGgttcttgttt ... atctttacagCTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 62 (downstream exon)
Score: 3

CACGCATGGTGTGCCTGCCCCAAGGAACAGCCACCCCCAATCTTCTGGTGCCGGCGATGAGTTCTTGGTCGTCCACAATGGCATCATCACAAACTACGAGgttcttgttt ... atctttacagCTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGCCAACATGTTATCTTCCAAGCCCTGCACATGGGCTGTCTCCAATCTCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctgatattgtactagaattcttgtatagtatttctctcatcatctttacagCTGGGGAATCCACATGCATTATTGCAACTATGGTGGATTTATGCTATTGGCCAACATGTTATCTTCCAAGCCCTGCACATGGGCTGTCTCCAATCTCCAT
  ttctgat  putative branch site (score: 3)
                                  tttctctcatcatctt  putative PPT
                           tatagtattt  TA-rich tract