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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattgaagccacattgccattagtatatatttcaagcttcctaaagagtttctctcctgatacttgtttttatgcctgcaatgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 22
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|86513451|gb|CI156084.1|CI156084
EST:     AAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|88690803|gb|CI734882.1|CI734882
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86480387|gb|CI123020.1|CI123020
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86597783|gb|CI274774.1|CI274774
EST:     CCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: CCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|87022912|gb|CI269848.1|CI269848
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86479218|gb|CI121851.1|CI121851
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86437517|gb|CI119239.1|CI119239
EST:     GTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: GTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|87035968|gb|CI190590.1|CI190590
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|87015009|gb|CI273407.1|CI273407
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|29683102|gb|CB679377.1|CB679377
EST:     AGGAGTTCCAAAACGTATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|87021468|gb|CI274075.1|CI274075
EST:     TGGGTACAGCTAGACATTGCCAAGGAGTTCCGAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: TGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86260839|gb|CI066514.1|CI066514
EST:     TACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: TACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|88340407|gb|CI659613.1|CI659613
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCAC
EST: gi|87030269|gb|CI270279.1|CI270279
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|5003387|gb|AU068536.1|AU068536
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86495201|gb|CI137834.1|CI137834
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|58690187|gb|CK078874.1|CK078874
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|87021432|gb|CI274039.1|CI274039
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|58661468|gb|CK050148.1|CK050148
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|87013826|gb|CI271217.1|CI271217
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|88691467|gb|CI733545.1|CI733545
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|29641075|gb|CB646082.1|CB646082
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86481939|gb|CI124572.1|CI124572
EST:     AAGCCATGTGGGTACAGCCAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|29671822|gb|CB668097.1|CB668097
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|87027363|gb|CI270038.1|CI270038
EST:     CCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: CCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|88688269|gb|CI731845.1|CI731845
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86596902|gb|CI270698.1|CI270698
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCAAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|29675673|gb|CB671948.1|CB671948
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         TTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|87032662|gb|CI270297.1|CI270297
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|218485492|gb|FG956827.1|FG956827
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86521397|gb|CI161603.1|CI161603
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86482562|gb|CI125195.1|CI125195
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86858379|gb|CI273007.1|CI273007
EST:     AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|86519938|gb|CI160144.1|CI160144
EST:     AGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: AGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
EST: gi|8860106|gb|AU097424.1|AU097424
EST:     ATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTT                         CTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC
genomic: ATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAAC

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: 73 (upstream exon), 74 (downstream exon)
Score: 143

GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattg ... aatgttgcagCTTCCAGCCGTCCTATCACTTTCGACGAAATTCGTTCCCACGATAATGAACATCCTGAAGAGATTAGCTGATGAGGGGCAGAGACCTGCAGCCCCAGAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCCCCTTTACCTGGGAGTCATATTTGTTGTTTTCCTTGTTGGAAAAGCCATGTGGGTACAGCTAGACATTGCCAAGGAGTTCCAAAATGGATTTgtaagtattgaagccacattgccattagtatatatttcaagcttcctaaagagtttctctcctgatacttgtttttatgcctgcaatgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG