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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcatttataattgccgcagtgtttctacatattttgagtggataatggttgctttatcatcttaagaattgtacttactatgaactctctttctgtagGAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAGTCTTAGTCATCTGAGGGCTCT

Basic information

species Oryza sativa
transcript LOC_Os01g48390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48390.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G078926_T01 (Zea mays), 3'ss of exon 2
---attcatttataattgccgcagtgtttctacatattttgagtggataatggttgctttatcatcttaagaattgtacttactatgaactctctttctgtagGAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAGTCTTAGTCATCTGAGGGCTCT
   |||  |||     ||| |  || ||| || ||| ||||  |     |||    | ||| |||||  || | | || ||| | |||||| ||||| |  || || || |||||||||||| ||||||| ||| | |||||||| ||||||| |||||| ||||||||||||||
ttaatttttttgctgctgcagttgtttttttatatactttggctattctatgt---cattagcatctggagtactctatttagtgtgaactatctttttccagAAACCTGAAGGATCTCTCATTAAGAGGCACCCTAGGTCCAGAGCTAGGAACTCTTAGCCATCTGAGGGCTCT
















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|29628097|gb|CB633108.1|CB633108
EST:     CCTTGCAGTTGGAACGGCGTCCGCTGCGTGGATGGCAGGGTGGTGATTCT                         GAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAG
genomic: CCTTGCAGTTGGAACGGCGTCCGCTGCGTGGATGGCAGGGTGGTGATTCTgtgagttcat ... ctttctgtagGAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAG
EST: gi|29630495|gb|CB635504.1|CB635504
EST:     CCTTGCAGTTGGAACGGCGTCCGCTGCGTGGATGGCAGGGTGGTGATTCT                         GAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAG
genomic: CCTTGCAGTTGGAACGGCGTCCGCTGCGTGGATGGCAGGGTGGTGATTCTgtgagttcat ... ctttctgtagGAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAG
EST: gi|29630295|gb|CB635304.1|CB635304
EST:     CCTTGCAGTTGGAACGGCGTCCGCTGCGTGGATGGCAGGGTGGTGATTCT                         GAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAG
genomic: CCTTGCAGTTGGAACGGCGTCCGCTGCGTGGATGGCAGGGTGGTGATTCTgtgagttcat ... ctttctgtagGAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggttgctttatcatcttaagaattgtacttactatgaactctctttctgtagGAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAGTCTTAGTCATCTGAGGGCTCT
                            tacttac  putative branch site (score: 1)
                                         ctctctttctgt  putative PPT
                  ttaagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcatttataattgccgcagtgtttctacatattttgagtggataatggttgctttatcatcttaagaattgtacttactatgaactctctttctgtagGAATCTAAAGGATCTCTCACTAAGAGGTACCTTGGGTCCAGAACTAGGAAGTCTTAGTCATCTGAGGGCTCT

- - - - - - -tgccgca
- - - - - - - - - - -tgtttct