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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatcactgtgattggaacttggaagataatgttgaacattactcactgcacatctttactgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGTTCTGCAAGCGTATATCTTTCAGTTGGTGGCATGCTATT

Basic information

species Oryza sativa
transcript LOC_Os02g17500.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G412899_T04 (Zea mays), 3'ss of exon 10
--------------------------------gtaagctatcactgtgattggaacttggaagataatgttgaacattactcactgcacatctttactgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGTTCTGCAAGCGTATATCTTTCAGTTGGTGGCATGCTATT
                                  ||   ||  |   || || ||     ||||  ||||||||||| ||| ||  |||   ||||||| ||||||| ||||||||||| |||||||||||||||||||| |||||  | |||||||||||| | ||||||||||||||||||||||| || ||
gtaagtgaccacgataaataacatttcctttataaaagaattgcaaagactgaaaaggcaaagaatatgttgaacatcacttacatcac---tttactggtatagGCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT
















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|29643521|gb|CB648528.1|CB648528
EST:     TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATG                         GCCTTTGCAATGGGACT
genomic: TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATGgtaagctatc ... actgctatagGCCTTTGCAATGGGACT
EST: gi|218501803|gb|FG948060.1|FG948060
EST:     TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATG                         GCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGT
genomic: TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATGgtaagctatc ... actgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGT
EST: gi|218493904|gb|FG949299.1|FG949299
EST:     TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATG                         GCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGT
genomic: TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATGgtaagctatc ... actgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGT
EST: gi|218498875|gb|FG949815.1|FG949815
EST:     TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATG                         GCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGT
genomic: TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATGgtaagctatc ... actgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGT
EST: gi|218496023|gb|FG951379.1|FG951379
EST:     TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATG                         GCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGT
genomic: TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATGgtaagctatc ... actgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGT
EST: gi|88732502|gb|CI755679.1|CI755679
EST:     TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATG                         GCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACC
genomic: TGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATGgtaagctatc ... actgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaacttggaagataatgttgaacattactcactgcacatctttactgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGTTCTGCAAGCGTATATCTTTCAGTTGGTGGCATGCTATT
                           tactcac  putative branch site (score: 1)
                                        tctttact  putative PPT
          aagataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctatcactgtgattggaacttggaagataatgttgaacattactcactgcacatctttactgctatagGCCTTTGCAATGGGACTTCAGGCTGTTGGAGCAAATCGTCACCACCTTGGTTCTGCAAGCGTATATCTTTCAGTTGGTGGCATGCTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG