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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacag

Basic information

species Oryza sativa
transcript LOC_Os06g45120.1
intron # 16
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|86261439|gb|CI017181.1|CI017181
EST:     CTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: CTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|218484409|gb|FG956802.1|FG956802
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29618245|gb|CB623257.1|CB623257
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29625786|gb|CB630797.1|CB630797
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|89178992|gb|CI043497.1|CI043497
EST:     CAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: CAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29613337|gb|CB618350.1|CB618350
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|33804193|gb|CF327971.1|CF327971
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGTGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|38477420|gb|CF961553.1|CF961553
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29617006|gb|CB622018.1|CB622018
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATCTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|88735905|gb|CI757480.1|CI757480
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTC
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTC
EST: gi|29629621|gb|CB634630.1|CB634630
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|87040164|gb|CI193373.1|CI193373
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|4715550|gb|AU056666.1|AU056666
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTCCTGNCCATTCTACAAGTCTGTTTGGATGATGCGCAACNT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29667460|gb|CB663735.1|CB663735
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29658784|gb|CB655059.1|CB655059
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATCTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|33804195|gb|CF327972.1|CF327972
EST:     AAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGTGCAACAT
genomic: AAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|87039264|gb|CI193886.1|CI193886
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29630925|gb|CB635934.1|CB635934
EST:     ACAGCCAAGCTATTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|86412469|gb|CI017337.1|CI017337
EST:     GCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: GCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29622588|gb|CB627599.1|CB627599
EST:     AGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: AGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29656412|gb|CB652687.1|CB652687
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|88337198|gb|CI628284.1|CI628284
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29626983|gb|CB631994.1|CB631994
EST:     ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: ACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT
EST: gi|29633886|gb|CB638895.1|CB638895
EST:     TGGCACAGAATGCATTTACCCC                         ATATGACAAGTTCTGTCCATTTTACAAGTCTGTTTGGATGATGCGCAACAT
genomic: TGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACAT

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: 57 (upstream exon), 56 (downstream exon)
Score: 60

CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcata ... aatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCCgtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA