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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaacatgtccctcattgaatttgaatgtataagtctatattgtggcctttactttaattgctatcatctttgctgctaataatatgtctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG

Basic information

species Oryza sativa
transcript LOC_Os06g49110.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49110.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ25898 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtaacatgtccctcattgaatttgaatgtataagtctatattgtggcctttactttaattgctatcatctttgctgctaataatatgtctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG
                                            |  |   || | || || || |  |  | | || | || |   | | ||   |  ||||  ||||||||||||| || ||||| || ||||||||||||||||| || || ||||| || |||||||
-------------------------------------------gtgatcatctcttctctagtttcggt--tttgtgatccttaacttctttccattccagGTGATCTACACGGATGTGGCACTGGATCCATATTCATCTGATGGTCACGACGGAATTGTGAGAGAAGATG
















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|29681115|gb|CB677390.1|CB677390
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29616370|gb|CB621382.1|CB621382
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29619108|gb|CB624120.1|CB624120
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29666981|gb|CB663256.1|CB663256
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29660427|gb|CB656702.1|CB656702
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29617546|gb|CB622558.1|CB622558
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29621569|gb|CB626580.1|CB626580
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29673911|gb|CB670186.1|CB670186
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29641824|gb|CB646831.1|CB646831
EST:     TTTGGTTCCACGGACTATTCGCCTGCTNCA-GGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: TTTGGTTCCACGGACTATTCGCCTGCT-CAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29687455|gb|CB683730.1|CB683730
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29672090|gb|CB668365.1|CB668365
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29661434|gb|CB657709.1|CB657709
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29641133|gb|CB646140.1|CB646140
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGACTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29679002|gb|CB675277.1|CB675277
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29619411|gb|CB624423.1|CB624423
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29667711|gb|CB663986.1|CB663986
EST:     TTTGGTTCCACGGACTATTCGCCTGCTNCA-GGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: TTTGGTTCCACGGACTATTCGCCTGCT-CAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29615586|gb|CB620598.1|CB620598
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29637162|gb|CB642171.1|CB642171
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29624060|gb|CB629071.1|CB629071
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29682583|gb|CB678858.1|CB678858
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29619315|gb|CB624327.1|CB624327
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|9788971|gb|BE530981.1|BE530981
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29643724|gb|CB648731.1|CB648731
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29655802|gb|CB652077.1|CB652077
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29637541|gb|CB642550.1|CB642550
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29681299|gb|CB677574.1|CB677574
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29688148|gb|CB684423.1|CB684423
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
EST: gi|29660273|gb|CB656548.1|CB656548
EST:     GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT                         GTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT
genomic: GTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATTgtaagtaaca ... tctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggcctttactttaattgctatcatctttgctgctaataatatgtctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG
      tttactttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaacatgtccctcattgaatttgaatgtataagtctatattgtggcctttactttaattgctatcatctttgctgctaataatatgtctgatttagGTTGTCTACACGGATGTTGCTCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG