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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctttgctcattgaaaattaatcttttgcgctgggcacttaatgtgccatattgcaatttgaatttgttagtagataaatatactctctttaacatatgattgcacatttgatcatattgaccttcactgttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTAATGCGGACGATATCTCCTCCGGCTGTGAAGTTCAGTGGCGCAAGTCCTT

Basic information

species Oryza sativa
transcript LOC_Os02g27360.1
intron # 9
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|86499644|gb|CI142277.1|CI142277
EST:     GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGCCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88562526|gb|CI493243.1|CI493243
EST:     TCGGGTGGGCAGATTACAGCT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: TCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|86493808|gb|CI136441.1|CI136441
EST:     GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88471689|gb|CI408960.1|CI408960
EST:     GTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88561222|gb|CI491939.1|CI491939
EST:     CTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: CTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88476517|gb|CI413788.1|CI413788
EST:     TCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: TCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88903097|gb|CI088635.1|CI088635
EST:     GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88373849|gb|CI508468.1|CI508468
EST:     TTTAGAAAATCAAGCTATCGGNTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: TTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88287873|gb|CI510153.1|CI510153
EST:     AATCNAGCTATCGGGTGGGCAGATTACAACT                         GGTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: AATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88246534|gb|CI246383.1|CI246383
EST:     GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88564859|gb|CI495576.1|CI495576
EST:     CTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: CTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88298083|gb|CI558488.1|CI558488
EST:     GCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88996348|gb|CI389059.1|CI389059
EST:     GTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88566507|gb|CI497224.1|CI497224
EST:     GGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88472773|gb|CI410044.1|CI410044
EST:     TCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: TCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88228038|gb|CI227518.1|CI227518
EST:     GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: GGTTCTTTATGATTTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88373848|gb|CI508467.1|CI508467
EST:     TTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACT                         GCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: TTAGAAAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
EST: gi|88373954|gb|CI508573.1|CI508573
EST:     AAATCAAGCTATCGGGTGGGCAGATTACAACT                         NCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA
genomic: AAATCAAGCTATCGGGTGGGCAGATTACAACTgtaagtcttt ... gttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctttaacatatgattgcacatttgatcatattgaccttcactgttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTAATGCGGACGATATCTCCTCCGGCTGTGAAGTTCAGTGGCGCAAGTCCTT
                               tattgac  putative branch site (score: 2)
                                              ttgtctc  putative PPT
     ttaacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctttgctcattgaaaattaatcttttgcgctgggcacttaatgtgccatattgcaatttgaatttgttagtagataaatatactctctttaacatatgattgcacatttgatcatattgaccttcactgttgtctcagGCTCCTCCAGCATTAAGATCAGTGATGACAAGGGATCAACATACACTGTTAATGCGGACGATATCTCCTCCGGCTGTGAAGTTCAGTGGCGCAAGTCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC