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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgataatttctccccatttgtttgttggttaagcagtcgattttttttttgaacctgcgggatgaacctgacgagagattttttctttggggttcagATCAAGGACATGGCGCTGAAGGCGTCGGGCGCGTACCGGCACTGCAAGCCGTGCGCCGGCTCGTCGTCGTCGTCACCGGCGGCGGGGGCGCGGCGGCACC

Basic information

species Oryza sativa
transcript LOC_Os08g36020.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G037941_T01 (Zea mays), 3'ss of exon 1
----tgttgataatttctccccatttgtttgttggttaagcagtcgattttttttttgaacctgcgggatgaacctgacgagagattttttctttggggttcagATCAAGGACATGGCGCTGAAGGCGTCGGGCGCGTACCGGCACTGCAAGCCGTGCGCCGGCTCGTCGTCGTCGTCACCGGCGGCGGGGGCGCGGCGGCACC
    | | |    |||||||  | | |    |   ||     | || | |      ||    || |   |     |||   ||||||||  | | ||  |||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| ||  || |  || ||  | ||  ||  | | || 
agcttttcgcaggtttctccaaaatcggc-atgctttgcttcgacggtgtgaagcgtgggtttg-gcactacgattgattggagatttt--cgtgggttttcagATCAAGGACATGGCGCTGAAGGCATCGGGCGCGTACCGGCACTGCAAGCCCTGCGCCGGTTCGTCCTCCCCGGCGGCGTCGCGGCGGCAGCAACCGTACT
















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|86909191|gb|CI302780.1|CI302780
EST:     AGTGCGCCACGCCCAGCACGAGGCAGGCCATCAAGGCGCTCACCGCCCAG                         ATCAAGGACATGGCGCTGAAGGCGTCGGGCGCGTACCGGCACTGCAAGCCG
genomic: AGTGCGCCACGCCCAGCACGAGGCAGGCCATCAAGGCGCTCACCGCCCAGgttggttact ... tggggttcagATCAAGGACATGGCGCTGAAGGCGTCGGGCGCGTACCGGCACTGCAAGCCG
EST: gi|88316690|gb|CI624132.1|CI624132
EST:     AGTGCGCCACGCCCAGCACGAGGCAGGCCATCAAGGCGCTCACCGCCCAT                         ATCAAGGACATGGCGCTGAAGGCGTCGGGCGCGTACCGGCACTGCAAGCCG
genomic: AGTGCGCCACGCCCAGCACGAGGCAGGCCATCAAGGCGCTCACCGCCCAGgttggttact ... tggggttcagATCAAGGACATGGCGCTGAAGGCGTCGGGCGCGTACCGGCACTGCAAGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttgaacctgcgggatgaacctgacgagagattttttctttggggttcagATCAAGGACATGGCGCTGAAGGCGTCGGGCGCGTACCGGCACTGCAAGCCGTGCGCCGGCTCGTCGTCGTCGTCACCGGCGGCGGGGGCGCGGCGGCACC
                       acctgac  putative branch site (score: 3)
                                    ttttttcttt  putative PPT
                                   attttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgataatttctccccatttgtttgttggttaagcagtcgattttttttttgaacctgcgggatgaacctgacgagagattttttctttggggttcagATCAAGGACATGGCGCTGAAGGCGTCGGGCGCGTACCGGCACTGCAAGCCGTGCGCCGGCTCGTCGTCGTCGTCACCGGCGGCGGGGGCGCGGCGGCACC

tgttgat
- - - - - ttctccc
- - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgcgg