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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCCTACCTACAACAAGCTAGGAAAGCATCTCCGTGGCATTGACTCCCTTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctgcttcctgttggttttggcagtttcacttcacttttctttgaactggatattagaaagtaaaatttggaggcacgaaatgaagagtttaat...

Basic information

species Oryza sativa
transcript LOC_Os02g01010.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01010.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G134889_T01 (Zea mays), 5'ss of exon 9
GGAGCCTACCTACAACAAGCTAGGAAAGCATCTCCGTGGCATTGACTCCCTTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctgcttcctgttggttttggcagt--ttcacttcacttttctttgaactggatattagaaagtaaaatttggaggcacgaaatgaagagtttaat--
||| ||||| |||||||| |||| |||||||| ||| | ||||||||||||| |||| ||||||||||| ||| ||||||||||||||||||||||||| ||| || ||| | |||| | | || | ||| ||||| || || | ||| | | | |||||
GGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtatcactacctttgaaggttggttttggctgaccatccattttcttgaa---aatgttttgctgccttgttttcttttat-atttattatttttaaaac

upper sequence: LOC_Os02g01010.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G033829_T02 (Zea mays), 5'ss of exon 10
GGAGCCTACCTACAACAAGCTAGGAAAGCATCTCCGTGGCATTGACTCCCTTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctgcttcct------gttggttttggcagtttcacttcacttttctttgaactggatattagaaagtaaaatttggaggcacgaaatgaagagtttaat
||||||||| |||||||| |||| |||||||| |||| ||||||||||||| ||||| ||||||||||| ||| ||||||||||||||||||||||||| ||| | || || |||||||||||| | | || |||| |||||| ||||| | ||| | | | | | | |||
GGAGCCTACTTACAACAAACTAGCCAAGCATCTAAGTGGAGTTGACTCCCTTGTGATAGCCAAAATGGATGGTACTACCAATGAGCATCCACGTGCAAAGgtttgtattactgccgtagatggttggttttggctgac---catccattttttttgaa--aaatattcttttttttc-tttatatttatcatttttaaaacttatc
















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|88908344|gb|CI090937.1|CI090937
EST:     CTAAAATGGATGGCACTGCCAATGAGNATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: CTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|86893336|gb|CI313437.1|CI313437
EST:     CATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: CATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|15849945|gb|BI798221.1|BI798221
EST:     TAATA-CTAAAATGGATGCCACT-CCAATGAGCATCCACGTCCAAA-                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|86546649|gb|CI186855.1|CI186855
EST:     TGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|15850569|gb|BI798845.1|BI798845
EST:     TTGTAATAGCTAAAATGGAT-GCACTGCCAATGAGCATCCACGT-CAAAG                         CCTGATGGATTCCCAACGATGCCTCTTTTATCCAGCAGGAAAGAAAAGTTT
genomic: TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGAT-CCTCTTTTATCCAGCAGGAAAGAAAAGTTT
EST: gi|89193503|gb|CI050801.1|CI050801
EST:     AGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: AGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|87034915|gb|CI188718.1|CI188718
EST:     TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|2797997|gb|AA751291.1|AA751291
EST:     CTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: CTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|66916422|gb|CX103270.1|CX103270
EST:     TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTAAAATCCAGCAGGAAAGAAA
genomic: TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAA
EST: gi|86545063|gb|CI185269.1|CI185269
EST:     GTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: GTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|29660339|gb|CB656614.1|CB656614
EST:     TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|86511920|gb|CI154553.1|CI154553
EST:     ATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: ATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|89184057|gb|CI046622.1|CI046622
EST:     TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|58681044|gb|CK069731.1|CK069731
EST:     TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|86493340|gb|CI135973.1|CI135973
EST:     TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|86509792|gb|CI152425.1|CI152425
EST:     TGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|88839098|gb|CI378022.1|CI378022
EST:     AGCTTAAATGGATGCCCCTGCCAATGAGCATCCACGTGCAAAG                         CCTGAT-GATTCCCAACGATCCTCTTTTATCCACCAGGAAAGAAAAGTTTT
genomic: AGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
EST: gi|88250194|gb|CI250471.1|CI250471
EST:     TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAG                         CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT
genomic: TTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTT

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: 74 (upstream exon), 69 (downstream exon)
Score: 68

GGAGCCTACCTACAACAAGCTAGGAAAGCATCTCCGTGGCATTGACTCCCTTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctg ... cttgtcacagCCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCCTACCTACAACAAGCTAGGAAAGCATCTCCGTGGCATTGACTCCCTTGTAATAGCTAAAATGGATGGCACTGCCAATGAGCATCCACGTGCAAAGgtctgttctgcttcctgttggttttggcagtttcacttcacttttctttgaactggatattagaaagtaaaatttggaggcacgaaatgaagagtttaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG