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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcatctgaatttttattcagtatctgtttattcacgaaattatctttgcctgatatgaactgaatttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGAACAGGATATTCAAATGCTTCCAAAGAAGGTTACCCTATCAACACAAAAA

Basic information

species Oryza sativa
transcript LOC_Os07g19190.1
intron # 3
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|29628204|gb|CB633215.1|CB633215
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|86260520|gb|CI066393.1|CI066393
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|14192515|gb|AU184726.1|AU184726
EST:     ACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: ACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|425829|gb|D22507.1|D22507
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|58688852|gb|CK077539.1|CK077539
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|88241618|gb|CI241467.1|CI241467
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|58675839|gb|CK064526.1|CK064526
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|3760617|gb|C97871.1|C97871
EST:     ACATGAACGGC-GAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: ACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|88213747|gb|CI213596.1|CI213596
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|88978643|gb|CI384984.1|CI384984
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|9865927|gb|AU101677.1|AU101677
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|88257346|gb|CI359734.1|CI359734
EST:     CAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|58030381|gb|CX727924.1|CX727924
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|58591169|gb|CF989477.1|CF989477
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGC
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGC
EST: gi|58589775|gb|CF988083.1|CF988083
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
EST: gi|86531386|gb|CI171592.1|CI171592
EST:     CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAG                         GCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA
genomic: CTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGA

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), 74 (downstream exon)
Score: 49

CAGAGCGCTATGACCGGAATGTCACTGAGCAAACACTTAAGGCTATCTCTCTTATTACAAAGATTAGACATGAACGGCAGAAGAAACATATTACAGAGAGgttggcatct ... tttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGAACAGGATATTCAAATGCTTCCAAAGAAGGTTACCCTATCAACACAAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatctgtttattcacgaaattatctttgcctgatatgaactgaatttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGAACAGGATATTCAAATGCTTCCAAAGAAGGTTACCCTATCAACACAAAAA
                            gcctgat  putative branch site (score: 49)
                                             ttttt  putative PPT
                                      aactgaatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcatctgaatttttattcagtatctgtttattcacgaaattatctttgcctgatatgaactgaatttttaacagGCAAAAACAGGGTAAGACAAAGCAACGGGAGAGGGATGCTAAGGAGTTGGAACAGGATATTCAAATGCTTCCAAAGAAGGTTACCCTATCAACACAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG