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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccatgattgtaatagccaattctgccagtttgagaaggatgctattgctctggattagccatgcatattttgtcttacacatcttttctggtatacagGCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATGAAAAAGGAAAACCCCCTGGAGTGTTAGGTTGGTGGCCTTCGCGTGCTGTCACATTTATAGAAA

Basic information

species Oryza sativa
transcript LOC_Os01g51754.2
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|88670301|gb|CI724417.1|CI724417
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGA
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGA
EST: gi|88670102|gb|CI724218.1|CI724218
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAG
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAG
EST: gi|29678996|gb|CB675271.1|CB675271
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATGAAAAAGGAAAACCC
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATGAAAAAGGAAAACCC
EST: gi|88671942|gb|CI726050.1|CI726050
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGAT
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGAT
EST: gi|88672210|gb|CI726326.1|CI726326
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGATCTGAGTACTGGCGT
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGATCTGAGTACTGGCGT
EST: gi|88672026|gb|CI726142.1|CI726142
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGATCTGAGTACTGGCGT
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGATCTGAGTACTGGCGT
EST: gi|88673425|gb|CI727538.1|CI727538
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGATC
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGATC
EST: gi|89172131|gb|CI721190.1|CI721190
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGATCTG
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGATCTG
EST: gi|88667110|gb|CI719246.1|CI719246
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATGAAAAAGGA
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATGAAAAAGGA
EST: gi|88669291|gb|CI719429.1|CI719429
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATG
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATG
EST: gi|88904363|gb|CI711671.1|CI711671
EST:     ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCT                         GCACTGGAAAGATCT
genomic: ATGGAACTGCTGGTGCATTTGATGTTACCACGAAAGGAATACTTCACTCTgtgagactcc ... tggtatacagGCACTGGAAAGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctctggattagccatgcatattttgtcttacacatcttttctggtatacagGCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATGAAAAAGGAAAACCCCCTGGAGTGTTAGGTTGGTGGCCTTCGCGTGCTGTCACATTTATAGAAA
                            gtcttac  putative branch site (score: 3)
                                    catcttttct  CT-rich tract
                     atattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccatgattgtaatagccaattctgccagtttgagaaggatgctattgctctggattagccatgcatattttgtcttacacatcttttctggtatacagGCACTGGAAAGATCTGAGTACTGGCGTCTGTCTGATGAAAAAGGAAAACCCCCTGGAGTGTTAGGTTGGTGGCCTTCGCGTGCTGTCACATTTATAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG