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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcacaggagatcttcagtttattccgtgcaacactgtgctatgtggatggattagtgttcagtgattgtaatccttgtaatattgtacctacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGTCAAGCAGCTGAGGAATCAAAGGTTGATTTACTGATCGTTGGGAGTCACA

Basic information

species Oryza sativa
transcript LOC_Os01g32780.1
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|86854099|gb|CI252090.1|CI252090
EST:     TTTCGCAGGCGCCCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88554825|gb|CI485033.1|CI485033
EST:     CAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: CAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88478954|gb|CI416225.1|CI416225
EST:     TTCGCAGGCGGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: CTCGCAGGC-GCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|86531544|gb|CI171750.1|CI171750
EST:     TTTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88451899|gb|CI694675.1|CI694675
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88514000|gb|CI441506.1|CI441506
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88352703|gb|CI678724.1|CI678724
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|218783418|gb|GE329470.1|GE329470
EST:     AGGCCAAGCAGATCTGCGCGCAGCAGGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGGGATGATATGT
genomic: AGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88205933|gb|CI205782.1|CI205782
EST:     TCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|58591025|gb|CF989333.1|CF989333
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAG
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAG
EST: gi|218485522|gb|FG954089.1|FG954089
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|86512186|gb|CI154819.1|CI154819
EST:     CGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: CGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|86253249|gb|CI058174.1|CI058174
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88239880|gb|CI239042.1|CI239042
EST:     CTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: CTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88543842|gb|CI473884.1|CI473884
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|55415560|gb|CV727936.1|CV727936
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88537466|gb|CI464415.1|CI464415
EST:     CGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: CGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|218502682|gb|FG963566.1|FG963566
EST:     TCTCGCAGGCGCTCCTCGACAATGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|13807126|gb|AU181815.1|AU181815
EST:     TCTNGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGNCAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88325391|gb|CI675189.1|CI675189
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAG
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAG
EST: gi|218488077|gb|FG946106.1|FG946106
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|218783473|gb|GE329525.1|GE329525
EST:     AGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: AGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|218499937|gb|FG948455.1|FG948455
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|38565622|gb|CK085075.1|CK085075
EST:     CAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: CAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|86824608|gb|CI264930.1|CI264930
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|86855742|gb|CI269069.1|CI269069
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88551228|gb|CI481266.1|CI481266
EST:     CTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: CTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|86512450|gb|CI155083.1|CI155083
EST:     TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAGGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|10930789|gb|AU161063.1|AU161063
EST:     TNTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGCCAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
EST: gi|88540143|gb|CI470163.1|CI470163
EST:     TCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGG                         GTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT
genomic: TCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGT

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: 75 (upstream exon), 70 (downstream exon)
Score: 15

CGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGCAGCAGCAGCTCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGCGCAGCATGGGgtatgtatta ... tacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGTCAAGCAGCTGAGGAATCAAAGGTTGATTTACTGATCGTTGGGAGTCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatggattagtgttcagtgattgtaatccttgtaatattgtacctacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGTCAAGCAGCTGAGGAATCAAAGGTTGATTTACTGATCGTTGGGAGTCACA
                              ttgtaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcacaggagatcttcagtttattccgtgcaacactgtgctatgtggatggattagtgttcagtgattgtaatccttgtaatattgtacctacaattcagGTGGCTGTAGAGACAATGATCAAAGTAGGAGATCCTAAGGAGATGATATGTCAAGCAGCTGAGGAATCAAAGGTTGATTTACTGATCGTTGGGAGTCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - ccgtgca
- - - - - - - - - - - - - - - - - ctgtgct
- - - - - - - - - - - - - - - - - - - - - -gtggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgt