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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaccaagtgcatcgtatattttatcattgaacccttcacaaatttcatcgaataattgttatatcttcatgacagaactctaatccatgctgtttttgttgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAATAATGCTCGTCATACAGGCAAAGAGGGGTTTTGCCTTCGGAGCCAGCGA

Basic information

species Oryza sativa
transcript LOC_Os01g42490.2
intron # 13
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|157650229|gb|EX449863.1|EX449863
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTANCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|86480117|gb|CI122750.1|CI122750
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTG-TTTNGTGAATTAGCATTCACAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTT-GTGAATTAGCATTCACAAA
EST: gi|87027334|gb|CI270009.1|CI270009
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|88457578|gb|CI536976.1|CI536976
EST:     CTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: CTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|29624406|gb|CB629417.1|CB629417
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|86858239|gb|CI271125.1|CI271125
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|88304669|gb|CI520524.1|CI520524
EST:     ATACCTTCCCGAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|29624470|gb|CB629481.1|CB629481
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|87013807|gb|CI271198.1|CI271198
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|58690956|gb|CK079643.1|CK079643
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|29624531|gb|CB629542.1|CB629542
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|58677956|gb|CK066643.1|CK066643
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATA
EST: gi|86480856|gb|CI123489.1|CI123489
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|29635013|gb|CB640022.1|CB640022
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|88901588|gb|CI001696.1|CI001696
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
EST: gi|29637193|gb|CB642202.1|CB642202
EST:     ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAG                         AAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA
genomic: ATACCTTCCCAAAAGAAATTCTGAAACAAACAATTGGGTTCCCTACCAAGgtatcaccaa ... tgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttatatcttcatgacagaactctaatccatgctgtttttgttgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAATAATGCTCGTCATACAGGCAAAGAGGGGTTTTGCCTTCGGAGCCAGCGA
                       ctctaat  putative branch site (score: 3)
                                      tttttgtt  putative PPT
     tatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcaccaagtgcatcgtatattttatcattgaacccttcacaaatttcatcgaataattgttatatcttcatgacagaactctaatccatgctgtttttgttgcttgacagAAATGGGGAAGTGATCATATCGCTTTGGTTTGTGAATTAGCATTCACAAAATAATGCTCGTCATACAGGCAAAGAGGGGTTTTGCCTTCGGAGCCAGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG