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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaaaactatgtcaggttgacaaacttttcttatagtggctttcaatcaattttttctttgtttaccttaactgactaacttttcaaacctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGATATGATACTTTTAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g33020.1
intron # 3
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|88478239|gb|CI415510.1|CI415510
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88832255|gb|CI017489.1|CI017489
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88956108|gb|CI092396.1|CI092396
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         CAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88513510|gb|CI441016.1|CI441016
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88968596|gb|CI098826.1|CI098826
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88988903|gb|CI040635.1|CI040635
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|86520090|gb|CI160296.1|CI160296
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|87028415|gb|CI263757.1|CI263757
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|89168502|gb|CI038856.1|CI038856
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88239868|gb|CI239030.1|CI239030
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         CAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACGTTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88479563|gb|CI416834.1|CI416834
EST:     GTGGAATATTTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGGTCAAAACATTGA
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATAT-GTCAAAACATTGA
EST: gi|86869390|gb|CI339114.1|CI339114
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         CAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|86544227|gb|CI184433.1|CI184433
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|87034968|gb|CI188771.1|CI188771
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCGATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88832263|gb|CI017497.1|CI017497
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|163928213|gb|EG712541.1|EG712541
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|86869388|gb|CI339112.1|CI339112
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         CAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88663760|gb|CI486063.1|CI486063
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|88424980|gb|CI562295.1|CI562295
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|9865647|gb|AU101397.1|AU101397
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATC-A                         -A-GTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|218485437|gb|FG946454.1|FG946454
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|89199179|gb|CI255445.1|CI255445
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|218488359|gb|FG945110.1|FG945110
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTACAATAAGCACCTTGATCAATATGTCAAAACA
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACA
EST: gi|88982282|gb|CI027859.1|CI027859
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGAT
EST: gi|58599380|gb|CK009908.1|CK009908
EST:     GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAA                         --G-TGCGAGCTTTTCAATAAGCAC
genomic: GTGGAATATGTTGTAAAAAATCCTTTGTACGCTCCTGGCACACCAATCAAgtaagctttc ... ctttcttaagCAGGTGCGAGCTTTTCAATAAGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcaattttttctttgtttaccttaactgactaacttttcaaacctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGATATGATACTTTTAGAG
                             gactaac  putative branch site (score: 1)
                                            cctttctt  putative PPT
     attttttctttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaaaactatgtcaggttgacaaacttttcttatagtggctttcaatcaattttttctttgtttaccttaactgactaacttttcaaacctttcttaagCAGGTGCGAGCTTTTCAATAAGCACCTTGATCAATATGTCAAAACATTGATATGATACTTTTAGAG

taaaaaa
- - - - - - - - - - acaaact
- - - - - - - - - - - - - - - - - - - -gctttca