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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcagaaatacccaatttgttaggttgaccacatgtccccattttgatctgcgacgtcacagacaattctcttgtaatgtatatgtgcattgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGAAGTAACCATCAACTGATCTAAGCTGGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g28989.5
intron # 1
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|29668997|gb|CB665272.1|CB665272
EST:     GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGT                         AAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
genomic: GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGTgtaagcgacc ... tgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
EST: gi|58597707|gb|CK008235.1|CK008235
EST:     GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGT                         AAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
genomic: GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGTgtaagcgacc ... tgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
EST: gi|58694230|gb|CK082917.1|CK082917
EST:     GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGT                         AAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
genomic: GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGTgtaagcgacc ... tgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
EST: gi|29623281|gb|CB628292.1|CB628292
EST:     GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGT                         AAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
genomic: GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGTgtaagcgacc ... tgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
EST: gi|33683399|gb|CF311638.1|CF311638
EST:     GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGT                         AAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
genomic: GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGTgtaagcgacc ... tgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
EST: gi|29671851|gb|CB668126.1|CB668126
EST:     GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGT                         AAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
genomic: GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGTgtaagcgacc ... tgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
EST: gi|29658148|gb|CB654423.1|CB654423
EST:     GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGT                         AAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA
genomic: GTCGTCGTCCTCCCCCGCCGATTACGAGTGCTACGTCCACTACACCGAGTgtaagcgacc ... tgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctgcgacgtcacagacaattctcttgtaatgtatatgtgcattgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGAAGTAACCATCAACTGATCTAAGCTGGGAG
 ttttgat  putative branch site (score: 4)
                             taatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcagaaatacccaatttgttaggttgaccacatgtccccattttgatctgcgacgtcacagacaattctcttgtaatgtatatgtgcattgtttgtcagAAACCTGTCGAATGGGAGGCACCATCATAATTATATGATCCAGCATTATGAAGTAACCATCAACTGATCTAAGCTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG