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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtttgtgtttaatttggggatgtttctgaattgtttccgtgcgtttcagattggggaatgctgtgtttcgccgagattttctcatcttccatatgtgatatcagattataattgtatgtgtttttgtttcgctgcaaattaattatattgatgcgaagtttctctgcatttgattgcagATTTTCGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCTTTTCTTGTCGCCGAAGATGGTGTCAGCAAATATACATCGACGCACATGA

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G045241_T03 (Zea mays), 3'ss of exon 2
gtgggtttgtgtttaatttggggatgtttctgaattgtttccgtgcgtttcagattggggaatgctgtgtttcgccgagattttctcatcttccatatgtgatatcagattataattgtatgtgtttttgtttcgctgcaaattaattatattgatgcgaag--tttctctgcatttg-attgcagATTTT-CGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCT-TTTCTTGTCGCCGAAGATGGTGTCAGCAAATATACATCGACGCACATGA-
||     ||| |||   |    ||  |     |    |     |     ||||  |  |   ||||  |||   ||   || |      |||   ||  |  | || |  |  |   |  |    || ||||  |   |||        |||||| || ||   ||  | | |  ||  |||||||||||| | ||||| |||||||||||| ||||  |||||||||||||  |||  ||| || | ||||   | ||| ||||| ||   | | |   |   |||| 
gtacaactgtttttcggtgcacgaaatgaaaaaccgatgcatatattcctcagggtttgct-tgcttagtt---cctgtatctcaatggcttgtttacttagtttctgtgtggaggagggtaatattatgttctgtaccaag-------tattgaagcaaatatttcttttactcttacattgcagATTTTTCCATGCACTTTAGGCTAAAAATGCTTTGGTCTGAAACCTATCTGCCCTTTTTTCTGGCCGCCAACGGTTTCAGCCAACGCATACCAGTG---ATGAA

upper sequence: LOC_Os03g63020.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G045241_T01 (Zea mays), 3'ss of exon 1
gtgggtttgtgtttaatttggggatgtttctgaattgtttccgtgcgtttcagattggggaatgctgtgtttcgccgagattttctcatcttccatatgtgatatcagattataattgtatgtgtttttgtttcgctgcaaattaattatattgatgcgaagtttctctgcatttg-attgcagATTTT-CGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCT-TTTCTTGTCGCCGAAGATGGTGTCAGCAAATATACATCGACGCACATGA-----------------------------------------
                                                                                                                                                                   |  | | |  ||  |||||||||||| | ||||| |||||||||||| ||||  |||||||||||||  |||  ||| || | ||||   | ||| ||||| ||   | | |   |   | ||                                         
-------------------------------------------------------------------------------------------------------------------------------------------------------------------tcttttactcttacattgcagatttttccatgcactttaggctaaaaatgctttggtctgaaacctatctgcccttttttctggccgccaacggtttcagCCAACGCATACCAGTGATGAAGATCTTCCGCTGAAGCTTGCTCAAGCTGCAATAAAGCATGACG

upper sequence: LOC_Os03g63020.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G045241_T02 (Zea mays), 3'ss of exon 1
gtgggtttgtgtttaatttggggatgtttctgaattgtttccgtgcgtttcagattggggaatgctgtgtttcgccgagattttctcatcttccatatgtgatatcagattataattgtatgtgtttttgtttcgctgcaaattaattatattgatgcgaag--tttctctgcatttg-attgcagATTTT-CGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCT-TTTCTTGTCGCCGAAGATGGTGTCAGCAAATATACATCGACGCACATGA-
                                                                               || |      |||   ||  |  | || |  |  |   |  |    || ||||  |   |||        |||||| || ||   ||  | | |  ||  |||||||||||| | ||||| |||||||||||| ||||  |||||||||||||  |||  ||| || | ||||   | ||| ||||| ||   | | |   |   |||| 
-------------------------------------------------------------------------------atctcaatggcttgtttacttagtttctgtgtggaggagggtaatattatgttctgtaccaag-------tattgaagcaaatatttcttttactcttacattgcagATTTTTCCATGCACTTTAGGCTAAAAATGCTTTGGTCTGAAACCTATCTGCCCTTTTTTCTGGCCGCCAACGGTTTCAGCCAACGCATACCAGTG---ATGAA

upper sequence: LOC_Os03g63020.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G045241_T04 (Zea mays), 3'ss of exon 1
gtgggtttgtgtttaatttggggatgtttctgaattgtttccgtgcgtttcagattggggaatgctgtgtttcgccgagattttctcatcttccatatgtgatatcagattataattgtatgtgtttttgtttcgctgcaaattaattatattgatgcgaagtttctctgcatttgattgcagATTTTCGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCTTTTCTTGTCGCCGAAGATGGTGTCAGCAAATATACATCGACGCACATGA
             |  |||     |   |   |  | ||||| |||  || ||  |    |||||| || |  |       | |  | | ||   |    |  | | | ||  |     | |  |    ||   | || | ||   ||    ||| ||    |    ||||| |  |         ||     |||  |       ||    ||  ||                                                                 
-------------tcttttactcttacattgcagatttttccatgcactttaggctaaa-aatgctttggtctgaaacctatctgcccttttttctggccgccaac-ggtttcagCCA-ACGCATACCAGT---GATGAAGATC--TTCCGCTGAAGCTTGCTCAAGCTGCAATAAAGCATGACGGTTGTGCACATAATGATGCTTAATCATTCATGTTGC--------------------------------------------------------------

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|88367674|gb|CI568446.1|CI568446
EST:     GTTCGGTGCGTTTTGGTTGAGGAATTTTGGCTCTAATTCGGTGCCATTAG                         ATTTTCGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCT
genomic: GTTCGGTGCGTTTTGGTTGAGGAATTTTGGCTCTAATTCGGTGCCATTAGgtgggtttgt ... ttgattgcagATTTTCGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCT
EST: gi|88718086|gb|CI741596.1|CI741596
EST:     GTTCGGTGCGTTTTGGTTGAGGAATTTTGGCTCTAATTCGGTGCCATTAG                         ATTTTCGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCT
genomic: GTTCGGTGCGTTTTGGTTGAGGAATTTTGGCTCTAATTCGGTGCCATTAGgtgggtttgt ... ttgattgcagATTTTCGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcgctgcaaattaattatattgatgcgaagtttctctgcatttgattgcagATTTTCGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCTTTTCTTGTCGCCGAAGATGGTGTCAGCAAATATACATCGACGCACATGA
           aaattaattatattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtttgtgtttaatttggggatgtttctgaattgtttccgtgcgtttcagattggggaatgctgtgtttcgccgagattttctcatcttccatatgtgatatcagattataattgtatgtgtttttgtttcgctgcaaattaattatattgatgcgaagtttctctgcatttgattgcagATTTTCGATGCATTTTAGGCTAAAAGTGCTCGGGTCTGAAACCTACGTGCTTTTCTTGTCGCCGAAGATGGTGTCAGCAAATATACATCGACGCACATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG