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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcaataacgttacaccaatgacaaaattgctggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaaccctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g44400.1
intron # 10
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|86899723|gb|CI327545.1|CI327545
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|55408882|gb|CV721258.1|CV721258
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|86834825|gb|CI345909.1|CI345909
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|313084043|gb|HO213826.1|HO213826
EST:     ACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|88449108|gb|CI560569.1|CI560569
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|86872687|gb|CI341897.1|CI341897
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|86843061|gb|CI342256.1|CI342256
EST:     TAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACACG                         CTGTGCACCCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCA
genomic: TAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACA-Ggtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCA
EST: gi|33821435|gb|CF336529.1|CF336529
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|29687876|gb|CB684151.1|CB684151
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|58589659|gb|CF987967.1|CF987967
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|38478016|gb|CF962149.1|CF962149
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCGGACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|58593409|gb|CF991717.1|CF991717
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|38473795|gb|CF957927.1|CF957927
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|27577571|gb|CB000266.1|CB000266
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|88528036|gb|CI456238.1|CI456238
EST:     CTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: CTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|88996530|gb|CI260034.1|CI260034
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|27548923|gb|CA767585.2|CA767585
EST:     ATAGTACGGGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|12623212|gb|AU173425.1|AU173425
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|29685102|gb|CB681377.1|CB681377
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|88993826|gb|CI112730.1|CI112730
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
EST: gi|33823734|gb|CF337673.1|CF337673
EST:     ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGTTACACAG                         CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT
genomic: ATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAGgtactcaata ... atttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaattgcaagcactacactcttggagtaactggtagctgaaaatttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG
                          gagtaac  putative branch site (score: 2)
                                              tttctgc  putative PPT
                                        tgaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcaataacgttacaccaatgacaaaattgctggatatgctgttagctatcatcagtgttttttcctgctgtaaaatcacaaccctgtatcacaaagccttgcaattgcaagcactacactcttggagtaactggtagctgaaaatttctgcagCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA