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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacatgttggattttattttggtgggatgtgcaatttacatcgaagtgtttaattacattatgtttcgattttttatcgcagGTTTGGAATTCTGATGAGCATGAGGATTTGCAGGTTATTGTGGTCATATCGCGCCCGCCTATCAAAGT

Basic information

species Oryza sativa
transcript LOC_Os12g34450.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G064371_T03 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------gtaaaacatgttggattttattttggtgggatgtgcaatttacatcga--------agtgtttaattac-attatgtttcgatttt----ttatcgcagGTTTGGAATTCTGATGAGCATGAGGATTTGCAGGTTATTGTGGTCATATCGCGCCCGCCTATCAAAGT
                                                                                  |   |  || | | | | ||  || |   | | |   || |   | ||        || |  || ||   | | | | ||   |||    || | |||||| ||||||||| ||||||| || |||||||| ||| ||||| ||||||||||||| ||  ||||  |
gtaaaagagaagggttgtcatttatatgcacttttactttgtctgatacagtgatatctcgtgtcctgatttgcacaactctgctgattatatggtactgtacctttgctagttttaagatattgttggagcttgggtagggcctatttgttagtgtctatcatctttctctttcttgcagGTCTGGAATTCTAATGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGCGCCCACCGGTCAAGAT

upper sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116204_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------------gtaaaacatgttggattttattttggtgggatgtgcaatttacatcgaagtgtttaattacattatgtttcgattttttatcgcagGTTTGGAATTCTGATGAGCATGAGGATTTGCAGGTTATTGTGGTCATATCGCGCCCGCCTATCAAAGT--------------------------------
                                                                                                 |  |||||||   | |||||||||||||| |  | |||| |  |       |||  |||   |||   ||   ||| | | |||||||||||||||||| ||||| || |||||||| ||| ||||| |||||||| | ||||||   ||  |                                
gtaaaggaaatgagttattacttatatgcatttttactttttctgatacattagatgcctcatatcctggttatatttaactgtaacttggccagatttcaacatgt--aaatttattttggtggg-taggaaattgatct-------ttttgttaatgtatacatcatctttctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGAGACCGCCTGCTAAGATGTGAGCATGCCTAACTTTAACATCGTGTTTCA

upper sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116204_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------------gtaaaacatgttggattttattttggtgggatgtgcaatttacatcgaagtgtttaattacattatgtttcgattttttatcgcagGTTTGGAATTCTGATGAGCATGAGGATTTGCAGGTTATTGTGGTCATATCGCGCCCGCCTATCAAAGT
                                                                                                 |  |||||||   | |||||||||||||| |  | |||| |  |       |||  |||   |||   ||   ||| | | |||||||||||||||||| ||||| || |||||||| ||| ||||| |||||||| | ||||||   ||  |
gtaaaggaaatgagttattacttatatgcatttttactttttctgatacattagatgcctcatatcctggttatatttaactgtaacttggccagatttcaacatgt--aaatttattttggtggg-taggaaattgatct-------ttttgttaatgtatacatcatctttctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGAGACCGCCTGCTAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcaatttacatcgaagtgtttaattacattatgtttcgattttttatcgcagGTTTGGAATTCTGATGAGCATGAGGATTTGCAGGTTATTGTGGTCATATCGCGCCCGCCTATCAAAGT
                    gtttaat  putative branch site (score: 4)
                                          ttttttatc  putative PPT
                     tttaattacattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacatgttggattttattttggtgggatgtgcaatttacatcgaagtgtttaattacattatgtttcgattttttatcgcagGTTTGGAATTCTGATGAGCATGAGGATTTGCAGGTTATTGTGGTCATATCGCGCCCGCCTATCAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT