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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaaaagggagctaacactagctgctgtgtgtttttacttcaatctttcagcacaagcacctttttctctttctctttttttttttgctaaaaaaatctggttacatttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA

Basic information

species Oryza sativa
transcript LOC_Os05g51190.4
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|58679376|gb|CK068063.1|CK068063
EST:     TGTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAG                         ATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
genomic: TGTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAGgtatcaaaag ... ttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
EST: gi|58681849|gb|CK070536.1|CK070536
EST:     TGTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAG                         ATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
genomic: TGTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAGgtatcaaaag ... ttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
EST: gi|58679423|gb|CK068110.1|CK068110
EST:     TGTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAG                         ATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
genomic: TGTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAGgtatcaaaag ... ttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
EST: gi|58662467|gb|CK051153.1|CK051153
EST:     GTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAG                         ATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
genomic: GTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAGgtatcaaaag ... ttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
EST: gi|38476078|gb|CF960211.1|CF960211
EST:     TGTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAG                         ATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
genomic: TGTGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAGgtatcaaaag ... ttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
EST: gi|86877342|gb|CI311548.1|CI311548
EST:     TGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAG                         ATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT
genomic: TGTAATCAAATGATGCTGAAACTTCGTGATTTTTATGATCCGAACAAGgtatcaaaag ... ttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctctttctctttttttttttgctaaaaaaatctggttacatttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA
                       tgctaaa  putative branch site (score: 2)
                                          cattttt  putative PPT
       tttctctttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcaaaagggagctaacactagctgctgtgtgtttttacttcaatctttcagcacaagcacctttttctctttctctttttttttttgctaaaaaaatctggttacatttttgtgtagATAATTACAAAACTTAAGGTTATCCCTGCATCTCCTGGTGGTGTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG