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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatctgactctatcaaaatctatattctgagcaactatttaggcattagaaagatgaacttatgactaaaatgtcgattctgtcaatgtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCTCCGCCTCACCTAGATGCGTCAATCGGGTTTAGTCTCGATTCATCGGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g70130.1
intron # 8
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|86434295|gb|CI094638.1|CI094638
EST:     CCTCAAGCTAAACCAAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: CCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|87040533|gb|CI195155.1|CI195155
EST:     GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|86593020|gb|CI270577.1|CI270577
EST:     GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCCAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACCAAACTCGAGAGGTTTCCT
genomic: GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|88198304|gb|CI198154.1|CI198154
EST:     GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|89162396|gb|CI104724.1|CI104724
EST:     AAGCTAAACCAAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: AAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|33795120|gb|CF323433.1|CF323433
EST:     GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|86500928|gb|CI143561.1|CI143561
EST:     GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCCAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|86500110|gb|CI142743.1|CI142743
EST:     GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCACAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|29615708|gb|CB620720.1|CB620720
EST:     GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: GCAGAGTATTTACTCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|88902688|gb|CI088226.1|CI088226
EST:     CTCAAGCTAAACCAAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: CTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
EST: gi|88964682|gb|CI070028.1|CI070028
EST:     TCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAAT                         ATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT
genomic: TCCAGATGTCAATAATAAGCCTCAAGCTAAACCAAATgtatgtttcc ... gtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattagaaagatgaacttatgactaaaatgtcgattctgtcaatgtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCTCCGCCTCACCTAGATGCGTCAATCGGGTTTAGTCTCGATTCATCGGCTG
                     gactaaa  putative branch site (score: 2)
                                              tatcttc  putative PPT
                      actaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatctgactctatcaaaatctatattctgagcaactatttaggcattagaaagatgaacttatgactaaaatgtcgattctgtcaatgtatcttcagATCCCAAGATTGGTGACAAGCACAAGCACAACAAAACTCGAGAGGTTTCCTCCGCCTCACCTAGATGCGTCAATCGGGTTTAGTCTCGATTCATCGGCTG

- - - - - - - atcaaaa
- - - - - - - - - - - - - attctga
- - - - - - - - - - - - - - - - - - - - - - - - - - -aagatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttatga